Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/64258)

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing 'fingerprints' of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591--8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3'-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be 'looped out' by small helix imperfections also show some reactivity.  (+info)

Endocytosis: EH domains lend a hand. (2/64258)

A number of proteins that have been implicated in endocytosis feature a conserved protein-interaction module known as an EH domain. The three-dimensional structure of an EH domain has recently been solved, and is likely to presage significant advances in understanding molecular mechanisms of endocytosis.  (+info)

Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D. (3/64258)

The crystal structure of profactor D, determined at 2.1 A resolution with an Rfree and an R-factor of 25.1 and 20.4%, respectively, displays highly flexible or disordered conformation for five regions: N-22, 71-76, 143-152, 187-193 and 215-223. A comparison with the structure of its mature serine protease, complement factor D, revealed major conformational changes in the similar regions. Comparisons with the zymogen-active enzyme pairs of chymotrypsinogen, trypsinogen and prethrombin-2 showed a similar distribution of the flexible regions. However, profactor D is the most flexible of the four, and its mature enzyme displays inactive, self-inhibited active site conformation. Examination of the surface properties of the N-terminus-binding pocket indicates that Ile16 may play the initial positioning role for the N-terminus, and Leu17 probably also helps in inducing the required conformational changes. This process, perhaps shared by most chymotrypsinogen-like zymogens, is followed by a factor D-unique step, the re-orientation of an external Arg218 to an internal position for salt-bridging with Asp189, leading to the generation of the self-inhibited factor D.  (+info)

Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. (4/64258)

Amyloid fibrils are assemblies of misfolded proteins and are associated with pathological conditions such as Alzheimer's disease and the spongiform encephalopathies. In the amyloid diseases, a diverse group of normally soluble proteins self-assemble to form insoluble fibrils. X-ray fibre diffraction studies have shown that the protofilament cores of fibrils formed from the various proteins all contain a cross-beta-scaffold, with beta-strands perpendicular and beta-sheets parallel to the fibre axis. We have determined the threedimensional structure of an amyloid fibril, formed by the SH3 domain of phosphatidylinositol-3'-kinase, using cryo-electron microscopy and image processing at 25 A resolution. The structure is a double helix of two protofilament pairs wound around a hollow core, with a helical crossover repeat of approximately 600 A and an axial subunit repeat of approximately 27 A. The native SH3 domain is too compact to fit into the fibril density, and must unfold to adopt a longer, thinner shape in the amyloid form. The 20x40-A protofilaments can only accommodate one pair of flat beta-sheets stacked against each other, with very little inter-strand twist. We propose a model for the polypeptide packing as a basis for understanding the structure of amyloid fibrils in general.  (+info)

Structural basis for the specificity of the initiation of HIV-1 reverse transcription. (5/64258)

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription requires specific recognition of the viral genome, tRNA3Lys, which acts as primer, and reverse transcriptase (RT). The specificity of this ternary complex is mediated by intricate interactions between HIV-1 RNA and tRNA3Lys, but remains poorly understood at the three-dimensional level. We used chemical probing to gain insight into the three-dimensional structure of the viral RNA-tRNA3Lys complex, and enzymatic footprinting to delineate regions interacting with RT. These and previous experimental data were used to derive a three-dimensional model of the initiation complex. The viral RNA and tRNA3Lys form a compact structure in which the two RNAs fold into distinct structural domains. The extended interactions between these molecules are not directly recognized by RT. Rather, they favor RT binding by preventing steric clashes between the nucleic acids and the polymerase and inducing a viral RNA-tRNA3Lys conformation which fits perfectly into the nucleic acid binding cleft of RT. Recognition of the 3' end of tRNA3Lys and of the first template nucleotides by RT is favored by a kink in the template strand promoted by the short junctions present in the previously established secondary structure.  (+info)

The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes. (6/64258)

Pax family transcription factors bind DNA through the paired domain. This domain, which is comprised of two helix-turn-helix motifs and a beta-hairpin structure, is a target of mutations in congenital disorders of mice and humans. Previously, we showed that Pax-5 (B-cell-specific activator protein) recruits proteins of the Ets proto-oncogene family to bind a composite DNA site that is essential for efficient transcription of the early-B-cell-specific mb-1 promoter. Here, evidence is provided for specific interactions between Ets-1 and the amino-terminal subdomains of Pax proteins. By tethering deletion fragments of Pax-5 to a heterologous DNA-binding domain, we show that 73 amino acids (amino acids 12 to 84) of its amino-terminal subdomain can recruit the ETS domain of Ets-1 to bind the composite site. Furthermore, an amino acid (Gln22) within the highly conserved beta-hairpin motif of Pax-5 is essential for efficient recruitment of Ets-1. The ability to recruit Ets proteins to bind DNA is a shared property of Pax proteins, as demonstrated by cooperative DNA binding of Ets-1 with sequences derived from the paired domains of Pax-2 and Pax-3. The strict conservation of sequences required for recruitment of Ets proteins suggests that Pax-Ets interactions are important for regulating transcription in diverse tissues during cellular differentiation.  (+info)

Identification of DNA polymorphisms associated with the V type alpha1-antitrypsin gene. (7/64258)

alpha1-Antitrypsin (alpha1-AT) is a highly polymorphic protein. The V allele of alpha1-AT has been shown to be associated with focal glomerulosclerosis (FGS) in Negroid and mixed race South African patients. To identify mutations and polymorphisms in the gene for the V allele of alpha1-AT in five South African patients with FGS nephrotic syndrome DNA sequence analysis and restriction fragment length polymorphisms of the coding exons were carried out. Four of the patients were heterozygous for the BstEII RFLP in exon III [M1(Val213)(Ala213)] and one patient was a M1(Ala213) homozygote. The mutation for the V allele was identified in exon II as Gly-148 (GGG)-->Arg (AGG) and in all patients was associated with a silent mutation at position 158 (AAC-->AAT). The patient who was homozygous for (Ala213) also had a silent mutation at position 256 in exon III (GAT-->GAC) which was not present in any of the other four patients. Although the V allele of alpha1-AT is not associated with severe plasma deficiency, it may be in linkage disequilibrium with other genes on chromosome 14 that predispose to FGS. Furthermore, the associated silent mutation at position 158 and the Ala213 polymorphism are of interest, as these could represent an evolutionary intermediate between the M1(Ala213) and M1(Val213) subtypes.  (+info)

Crystal structures of two H-2Db/glycopeptide complexes suggest a molecular basis for CTL cross-reactivity. (8/64258)

Two synthetic O-GlcNAc-bearing peptides that elicit H-2Db-restricted glycopeptide-specific cytotoxic T cells (CTL) have been shown to display nonreciprocal patterns of cross-reactivity. Here, we present the crystal structures of the H-2Db glycopeptide complexes to 2.85 A resolution or better. In both cases, the glycan is solvent exposed and available for direct recognition by the T cell receptor (TCR). We have modeled the complex formed between the MHC-glycopeptide complexes and their respective TCRs, showing that a single saccharide residue can be accommodated in the standard TCR-MHC geometry. The models also reveal a possible molecular basis for the observed cross-reactivity patterns of the CTL clones, which appear to be influenced by the length of the CDR3 loop and the nature of the immunizing ligand.  (+info)

1812.00995] Computational Chemistry as Voodoo Quantum Mechanics : Models, Parameterization, and Software1812.00995] Computational Chemistry as Voodoo Quantum Mechanics : Models, Parameterization, and Software
Abstract: Computational chemistry grew in a new era of desktop modeling, which coincided with a growing demand for modeling software, especially from the pharmaceutical industry. Parameterization of models in computational chemistry is an arduous enterprise, and we argue that this activity leads, in this specific context, to tensions among scientists regarding the lack of epistemic transparency of parameterized methods and the software implementing them. To explicit these tensions, we rely on a corpus which is suited for revealing them, namely the Computational Chemistry mailing List (CCL), a professional scientific discussion forum. We relate one flame war from this corpus in order to assess in detail the relationships between modeling methods, parameterization, software and the various forms of their enclosure or disclosure. Our claim is that parameterization issues are a source of epistemic opacity and that this opacity is entangled in methods and software alike. Models and software must be ...
http://export.arxiv.org/abs/1812.00995
Bioforum] ACS Short Course in Computational Chemistry and Drug DesignBioforum] ACS Short Course in Computational Chemistry and Drug Design
ACS Short Course Computational Chemistry and Computer-Assisted Drug Design: Practical Approaches 230th ACS National Meeting Washington Convention Center, Washington, DC Friday-Saturday, August 26-27, 2005 This introductory level course is designed for organic chemists, pharmaceutical chemists, and biochemists who are interested in learning more about computational and combinatorial methods, or scientists who need to develop a working knowledge of the fundamentals and need to understand the concepts and terminology of this rapidly developing area. Program Overview of Computational Chemistry and Computer-Assisted Drug Design Molecular Mechanics: Background, Development, Concepts, Force Fields Conformational Searching Molecular Dynamics Simulations: Background, Development, Concepts, and Applications Protein Structure Prediction Overview of Quantum Chemistry Methods and Its Application to Drug Design DNA and Protein Sequence and Structure Analysis Drug Design Methods and Pharmacophore Design QSAR ...
http://www.bio.net/bionet/mm/bioforum/2005-July/035336.html
Computational Chemistry Highlights: 2014Computational Chemistry Highlights: 2014
Around 20% of all the computational chemistry papers published in 2014 emanate from the USA, more than double the closest competitor, China. The top ten nations in terms of publications are USA 19.5%, China 9.3%, Germany 6.1%, India 4.3%, France 4.0%, Italy 3.8%, Spain 3.7%, England 3.6%, Japan 2.7% and Canada 2.4% - making nearly 60% of the total output. A decade ago in 2004 the ten most prolific countries accounted for around 87% of total output, which indicates that recent years have witnessed a greater global involvement in computational chemistry. Noticeable trends are seen in individual nations share of the computational chemistry pie, with the USA and some European nations effectively halving their fraction of papers between 2004 and 2014, with Chinas output nearly doubling from 5.4% in 2004 to 9.3% in 2014 and the emergence of India from outside the top ten into fourth place in 2014. It should be borne in mind that the globalization of science will inevitably lead to some over counting ...
http://www.compchemhighlights.org/2014/
中国科学院青岛生物能源与过程研究所机构知识库(QIBEBT-IR): Direct Observation of CH/CH van der Waals Interactions in Proteins by NMR中国科学院青岛生物能源与过程研究所机构知识库(QIBEBT-IR): Direct Observation of CH/CH van der Waals Interactions in Proteins by NMR
van der Waals interactions are important to protein stability and function. These interactions are usually identified empirically based on protein 3D structures. In this work, we performed a solution nuclear magnetic resonance (NMR) spectroscopy study of van der Waals interactions by detecting the through-space (vdw)J(CC)-coupling between protein aliphatic side chain groups. Specifically, (vdw)J(CC)-coupling values up to similar to 0.5 Hz were obtained between the methyl and nearby aliphatic groups in protein GB3, providing direct experimental evidence for the van der Waals interactions. Quantum mechanical calculations suggest that the J-coupling is correlated with the exchange-repulsion term of van der Waals interaction. NMR detection of (vdw)J(CC)-coupling offers a new tool to characterize such interactions in proteins ...
http://ir.qibebt.ac.cn/handle/337004/10686
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets | BMC...Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets | BMC...
Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pockets boundaries. For a set of conformationally
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-39/figures/10
Computational chemistry can bought by the day - LabHomepageComputational chemistry can bought by the day - LabHomepage
A SERVICE to enable researchers to outsource computational chemistry has been introduced by Cresset, a software company. Its CompChem on Demand offering supplies computational chemistry services on a day-by-day basis, without long-term commitment.. Users of the service can purchase service days in advance, at a discounted on the daily rate, and use these as needed. Cressets service team, under director of consulting Dr Martin Slater, offers a range of skills including the design of both large and small molecular libraries, lead optimisation, and structure-activity relationship (SAR) analysis.. The services provided will make use of Cressets commercially-available software, if appropriate, as well as the companys in-house proprietary code and applications.. The financial reality of drug discovery demands that researchers minimise costs while maximising throughput and efficiency, said Dr Robert Scoffin, CEO of Cresset. Through our on-demand consulting service, customers are able to match ...
http://labhomepage.com/429/consultancy-services/computational-chemistry-can-bought-by-the-day/
Protein-peptide molecular docking with large-scale conformational changes | Laboratory of Theory of BiopolymersProtein-peptide molecular docking with large-scale conformational changes | Laboratory of Theory of Biopolymers
Check out our new paper and video on Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction. ...
http://biocomp.chem.uw.edu.pl/protein-peptide-molecular-docking-large-scale-conformational-changes
Essentials of computational chemistry theories and models pdf
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http://www.berbervandenberg.tk/essentials-of-computational-chemistry-theories-and-models-pdf
16.08.28 Theory and Applications of Computational Chemistry 201616.08.28 Theory and Applications of Computational Chemistry 2016
16.08.28 Theory and Applications of Computational Chemistry 2016, Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
http://ccl.net/cca/info/conferencelist/mess0022272.shtml
17.11.06 Computational Chemistry and Biology Opportunities at D. E. Shaw Research17.11.06 Computational Chemistry and Biology Opportunities at D. E. Shaw Research
17.11.06 Computational Chemistry and Biology Opportunities at D. E. Shaw Research, Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
http://ccl.net/cca/jobs/joblist/mess0042884.shtml
Optimization of predictive energy landscapes for membrane and globular protein structure predictionOptimization of predictive energy landscapes for membrane and globular protein structure prediction
This thesis discusses recent results using the Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), an optimized, coarse-grained molecular dynamics model. AWSEM and its membrane protein extension, AWSEM-membrane, are capable of de novo protein structure prediction and through the use of statistical estimators, allow construction of free energy landscapes which can provide insight about the dynamics of protein systems. We review the origins of energy landscape theory and how one can learn energy functions using the results of spin glass-inspired statistical mechanics models. We explore the similarities and differences between the energy landscapes of proteins that have been selected by nature and those of some proteins designed by humans. We also study how robust the folding of these designs would be to the simplification of the sequences using fewer amino acid types. Using an optimized extension of AWSEM, AWSEM-membrane, we explore the hypothesis that the folding landscapes of ...
https://scholarship.rice.edu/handle/1911/88336
Foreword: Applied computational chemistry - Chemical Society Reviews (RSC Publishing)Foreword: Applied computational chemistry - Chemical Society Reviews (RSC Publishing)
A foreword from Professor Kendall N. Houk for the Applied Computational Chemistry themed issue of Chemical Society Reviews. Applied Computational Chemistry
http://pubs.rsc.org/en/Content/ArticleLanding/2014/CS/C4CS90049A?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+rss%2FCS+%28RSC+-+Chem.+Soc.+Rev.+latest+articles%29
Low frequency motions in proteins secondary structures. Molecular dynamics studies on carboxy terminal fragment of L7/L12...Low frequency motions in proteins secondary structures. Molecular dynamics studies on carboxy terminal fragment of L7/L12...
TY - CHAP. T1 - Low frequency motions in proteins secondary structures. Molecular dynamics studies on carboxy terminal fragment of L7/L12 ribosomal protein. AU - Tapia, O.. AU - Nilsson, O.. AU - Campillo, M.. AU - Aqvist, J.. AU - Horjales, E.. PY - 1990/1/1. Y1 - 1990/1/1. M3 - Chapter. SN - 0-940030-30-6. VL - 2. T3 - DNA Protein complexes & Proteins. SP - 147. EP - 170. BT - Structure & methods: proceedings of the Sixth Conversation in the Discipline Biomolecular Stereodynamics. Volume 2 DNA protein complexes & proteins. A2 - Ramaswamy H. Sarma, null. A2 - Mutki H. Sarma, null. PB - Adenine Press. CY - Schenectady (US). ER - ...
https://portalrecerca.uab.cat/en/publications/low-frequency-motions-in-proteins-secondary-structures-molecular--2
Check for Short Interatomic Distances
In this server, all interatomic distances between non-bonded atoms are calculated, and verified against these rules. If two atoms do come closer, the amount by which the contact is too close is printed in a table. In the table it will be indicated whether the bump is between symmetry relatives (inter) or within the given asymmetric unit (intra). A bump will never be reported between two atoms for which the sum of their atomic occupancies is less than 1.0 ...
https://swift.cmbi.umcn.nl/servers/html/bumps.html
Utilization of Protein Tertiary Contacts to Improve Protein Structure by Trung Thanh NguyenUtilization of Protein Tertiary Contacts to Improve Protein Structure by Trung Thanh Nguyen
The structure of a protein ultimately determines its function; therefore, knowledge of three-dimensional structure is essential for understanding its function and mechanism of action. The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. These methods are quite successful but can be very time-intensive and costly. An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. In this research, we attempted to determine if certain protein structure features, known as tertiary contacts, can improve the prediction of protein three-dimensional structure. By calculating and analyzing sequence homology and related values, it was shown that tertiary contacts, which typically are long-range amino acid interactions
https://scholarworks.sjsu.edu/etd_theses/4245/
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates | BMC Bioinformatics |...LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates | BMC Bioinformatics |...
Successful protein structure prediction requires accurate low-resolution scoring functions so that protein main chain conformations that are close to the native can be identified. Once that is accomplished, a more detailed and time-consuming treatment to produce all-atom models can be undertaken. The earliest low-resolution scoring used simple distance-based contact potentials, but more recently, the relative orientations of interacting amino acids have been taken into account to improve performance. We developed a new knowledge-based scoring function, LoCo, that locates the interaction partners of each individual residue within a local coordinate system based only on the position of its main chain N, Cα and C atoms. LoCo was trained on a large set of experimentally determined structures and optimized using standard sets of modeled structures, or decoys. No structure used to train or optimize the function was included among those used to test it. When tested against 29 other published main chain
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-368/figures/3
Computational Chemistry and Molecular Modeling Support GroupComputational Chemistry and Molecular Modeling Support Group
The Computational Chemistry and Molecular Modeling Support Group helps intramural researchers create structural models of biomolecules when X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or mass spectrometry data isnt available. By combining computer-based techniques with experimental and theoretical structural information, the group is able to develop structures that mimic the behavior of molecules or molecular reactions ...
https://www.niehs.nih.gov/research/atniehs/facilities/compmole/
Secondary structure prediction of β-subunits of the gonadotropin-thyrotropin family from its aligned sequences using...
TY - JOUR. T1 - Secondary structure prediction of β-subunits of the gonadotropin-thyrotropin family from its aligned sequences using environment-dependent amino-acid substitution tables and conformational propensities. AU - Wako, Hiroshi. AU - Ishii, Susumu. PY - 1995/2/22. Y1 - 1995/2/22. N2 - The secondary structures of β-subunits of the glycoprotein hormone family, LH (luteinizing hormone), CG (chorionic gonadotropin), FSH (follicle stimulating hormone), TSH (thyroid stimulating hormone), and GTH I/GTH II (two types of fish gonadotropins), are predicted by comparing an amino-acid substitution pattern at equivalent sites in their aligned sequences with environment-dependent amino-acid substitution tables and conformational propensities calculated from other protein families whose three-dimensional structures are known. According to the prediction results, together with other structural information obtained from experiments, the following points come up as important structural features of the ...
https://waseda.pure.elsevier.com/en/publications/secondary-structure-prediction-of-%CE%B2-subunits-of-the-gonadotropin-
Computational Chemistry Group - Kästner Group | Institut für Theoretische Chemie | University of StuttgartComputational Chemistry Group - Kästner Group | Institut für Theoretische Chemie | University of Stuttgart
Main Page of the Computational Chemistry Group. Scientific interests: Free Energy calculations, QM/MM method, PAW-method, Biological Nitrogen Fixation by Nitrogenase, sodium nitroprusside
http://www.uni-stuttgart.de/theochem/groups/kaestner/
Blind protein structure predictions from CASP3 and CASP4
Blind protein structure predictions from CASP3 and CASP4. A: Left, crystal structure of the MarA transcription factor bound to DNA; right, our best submitted model in CASP3. Despite many incorrect details, the overall fold is predicted with sufficient accuracy to allow insights into the mode of DNA binding. B: Left, the crystal structure of bacteriocin AS-48; middle, our best submitted model in CASP4; right, a structurally and functionally related protein (NK-lysin) identified using this model in a structure-based search of the Protein Data Bank (PDB). The structural and functional similarity is not recognizable using sequence comparison methods (the identity between the two sequences is only 5 percent). C: Left, crystal structure of the second domain of MutS; middle, our best submitted model for this domain in CASP4; right, a structurally related protein (RuvC) with a related function recognized using the model in a structure-based search of the PDB. The similarity was not recognized using ...
https://ralph.bakerlab.org/rah/rah_prediction.php
Use of non-crystallographic symmetry in protein structure refinementUse of non-crystallographic symmetry in protein structure refinement
Several methods to assess the (dis)similarity of protein structures objectively are described, some of which, when applied to non-crystallographically related protein models, are able to discriminate between significant differences and random noise. Some of these methods have been used to investigate a sample of several hundred protein structures which have been solved by means of X-ray crystallography in order to investigate the extent to which non-crystallographically related protein models differ from one another. It is shown that the extent of such differences is largely dependent on the resolution of the data used for the determination and refinement of the structure and, measured by some statistics, even varies essentially linearly with the resolution. The implications of these findings for the strategies used to refine structures with non-crystallographic symmetry, in particular at low resolution, are discussed. Finally, two examples are given of recent structure determinations from ...
http://uu.diva-portal.org/smash/record.jsf?pid=diva2:108035
Internformat: Prediction of protonation states in ligand-protein complexes upon ligand bindingInternformat: Prediction of protonation states in ligand-protein complexes upon ligand binding
diss/z2006/0801 Prediction of protonation states in ligand-protein complexes upon ligand binding Recent hardware development increase the computing power, in consequence many biological and chemical processes can now be successfully modelled in a way which was not to imagine 20 years ago. Examples of such processes are molecular dynamics studies of large biomolecules, the prediction of free energy of binding for protein-ligand complexes, investigations of reaction paths in enzymes, to mention only a few. One issue which is still unresolved concerns the accurate estimation of protonation states in protein-ligand complexes. In this thesis, we present the development of a novel charge assignment procedure named PEOE_PB (Partial Equalisation of Orbital Electronegativities - optimized for Poisson-Boltzmann calculations), which represents a method for the assignment of atomic partial charges. It works reliably with both proteins and small organic molecules using a consistent approach. Such charges are ...
http://archiv.ub.uni-marburg.de/ubfind/Record/urn:nbn:de:hebis:04-z2006-0801/Details
An Efficient Null Model for Conformational Fluctuations in Proteins - DTU OrbitAn Efficient Null Model for Conformational Fluctuations in Proteins - DTU Orbit
Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide bridges. The choice of the restraints themselves is heuristic, but the resulting probabilistic model is well-defined and rigorous. Conceptually, TYPHON constitutes a null model of conformational fluctuations under a given set of restraints. We demonstrate that TYPHON can provide information on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a ...
http://orbit.dtu.dk/en/publications/an-efficient-null-model-for-conformational-fluctuations-in-proteins
Download A Structural Framework For The Pricing Of Corporate Securities: Economic And Empirical Issues 2006
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http://martin-horn.com/book/download-A-Structural-Framework-for-the-Pricing-of-Corporate-Securities%3A-Economic-and-Empirical-Issues-2006.php
Theoretical and Computational Chemistry - Study - Cardiff UniversityTheoretical and Computational Chemistry - Study - Cardiff University
The School of Chemistry has developed a particular strength in Theoretical and Computational Chemistry, with a research group dedicated to this exciting area of study. As part of the Chemistry (PhD/MPhil) programme, students can conduct their research within this group.
http://www.cardiff.ac.uk/study/postgraduate/research/programmes/area/theoretical-and-computational-chemistry
TCR Scanning of Peptide/MHC through Complementary Matching of Receptor and Ligand Molecular Flexibility | The Journal of...TCR Scanning of Peptide/MHC through Complementary Matching of Receptor and Ligand Molecular Flexibility | The Journal of...
Although conformational changes in TCRs and peptide Ags presented by MHC protein (pMHC) molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. In this study, we used nuclear magnetic resonance to study TCR-pMHC binding, examining recognition of the QL9/H-2Ld complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR-pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR-pMHC complex. Determination of conformational exchange kinetics revealed that the motions of CDR3β and QL9 are closely matched. The matching of conformational exchange in the free proteins and its persistence in the complex enhances the thermodynamic and kinetic stability of the TCR-pMHC complex and provides a mechanism for facile binding. We thus propose that matching of structural ...
http://www.jimmunol.org/content/192/6/2885.short
Computational Chemistry PhD Projects, Programs & Scholarships in the UKComputational Chemistry PhD Projects, Programs & Scholarships in the UK
FindAPhD. Search Funded PhD Projects, Programs & Scholarships in Computational Chemistry in the UK. Search for PhD funding, scholarships & studentships in the UK, Europe and around the world.
https://www.findaphd.com/phds/united-kingdom/computational-chemistry/self-funded/?i1gE6CM0
MSc in Theoretical and Computational Chemistry | University of OxfordMSc in Theoretical and Computational Chemistry | University of Oxford
About the courseThe three primary activities in theoretical and computational chemistry are development of new theory, implementation of methods as reliable software, and application of such methods to a host of challenges in chemical and related sciences. The MSc aims to train new research students to be able to deliver these outcomes.
https://www.ox.ac.uk/admissions/graduate/courses/msc-theoretical-and-computational-chemistry-stand-alone?wssl=1
Linear-Scaling Techniques in Computational Chemistry and Physics | SpringerLinkLinear-Scaling Techniques in Computational Chemistry and Physics | SpringerLink
Computational chemistry methods have become increasingly important in recent years, as manifested by their rapidly extending applications in a large number of diverse fields. The ever-increasing size
https://link.springer.com/book/10.1007%2F978-90-481-2853-2
Experimental and theoretical studies of the molecular and crystal structures of trialkoxy- and chlorodialkoxy-stibanes
The molecular structures of triisopropoxystibane, Sb((OPr)-Pr-i)(3), and chlorodiisopropoxystibane, SbCl((OPr)-Pr-i)(2), were determined in the solid state by single crystal X-ray diffraction. Sb((OPr)-Pr-i)(3) forms discrete centrosymmetric dimers in the solid state via Sb . . .O-Sb interactions, leading to pseudo trigonal bipyramidal configurations of the four co-ordinate Sb atoms, while SbCl((OPr)-Pr-i)(2) forms chains via Sb . . .O-Sb and Sb . . . Cl-Sb bridges, resulting in five-co-ordinate Sb atoms with pseudo octahedral configurations. Comparison of the solid state structures and the density functional optimized molecular structures of Sb(OMe)(3), SbCl(OMe)(2) and their dimers revealed a steady increase of the average Sb-O bond lengths with the co-ordination number of Sb, and mutual trans effects of the ligands. Standard enthalpies of dimer formation from density functional calculations are -23.8 and -69.7 kJ mol(-1) for [Sb-2(mu -OMe)(2)(OMe)(4)] and [Sb2Cl2(mu -OMe)(2)(OMe)(2)], ...
https://pub.uni-bielefeld.de/publication/1928859
CECAM - Understanding function of proteins in membrane by atomistic and multiscale simulations
To understand the way a protein functions it is important to consider its cellular environment. About 25 % of genes encode membrane proteins, and furthermore membrane proteins are targets for ~50 % of marketed drugs. Signalling mechanisms of membrane receptors involve subtle conformational changes of these proteins [1]. Therefore it is of paramount importance from a biological and pharmaceutical point of view to elucidate the dynamics of these macromolecules in their native lipid environment. The use of molecular dynamics (MD) simulations represents the first natural choice to investigate such functional dynamics [2,3], providing an atomistic description of the interactions at work. Furthermore, the growing number of experimental structures released over the last fifteen years has represented a further stimulus for computational investigations [4]. Thus, taking also advantage of modern hardware we may enhance our understanding of membrane protein functions and the role of specific lipid/protein ...
https://www.cecam.org/workshop-details/487
Analysis of allosteric effect of pathologic variants at the light of local protein conformations - Inserm
Proteins are highly dynamic macromolecules. To analyze their inherent flexibility, computational biologists often use molecular dynamics (MD) simulations. The quantification of protein flexibility is based on various methods such as Root Mean Square Fluctuations (RMSF) that rely on multiple MD snapshots or Normal Mode Analysis (NMA) that rely on a single structure and focus on quantifying large movements. Alternative in silico approaches assess protein motions through the protein residue network or dynamical correlations from MD simulations. An alternative yet powerful approach based on small prototypes or structural alphabets (SAs) can be used. SAs approximate conformations of protein backbones and code the local structures of proteins as one-dimensional sequences. Protein Blocks (PBs) are one of these SAs. Applying PB-based approaches to biological systems such as the DARC protein, the human αIIb β3 integrin and the KISSR1 protein highlighted the major interest of PBs in understanding local
https://www.hal.inserm.fr/inserm-01853665
A high-level ab initio study of the N2 + N2 reaction channel - Pacifici - 2013 - Journal of Computational Chemistry - Wiley...A high-level ab initio study of the N2 + N2 reaction channel - Pacifici - 2013 - Journal of Computational Chemistry - Wiley...
system governing collisional processes, including N atom exchange. The related potential energy values were determined using high-level ab initio methods. The calculations were performed at a coupled-cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4-atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator. © 2013 Wiley Periodicals, Inc. ...
http://onlinelibrary.wiley.com/doi/10.1002/jcc.23415/full
The effect of solvation on biomolecular conformation: 2-Amino-1-phenylethanolThe effect of solvation on biomolecular conformation: 2-Amino-1-phenylethanol
Here we address this problem by using molecular mechanics simulations to build up a detailed picture of the conformational behavior of 2-amino-1-phenylethanol, a noradrenaline analogue, in aqueous solution in both its neutral and protonated forms. For the sake of comparison, equivalent simulations are also performed on the gas-phase molecules and gas-phase hydrated clusters. These calculations reveal the important role that water has to play in determining the conformational preferences and dynamic behavior of the molecules. Water molecules are found to bridge between the various functional groups within the molecule, significantly affecting their relative stabilities in comparison to the gas-phase values. The reorganization of these solvation structures also provides a mechanism for conformational interconversion. The role of the solvent in mediating interactions between the various functional groups within the molecule suggests that in noradrenaline the catechol groups will be able to ...
https://uobrep.openrepository.com/handle/10547/294864
Identification of Structural Signatures Within Transcription Factor Bi by Katharina SchulzeIdentification of Structural Signatures Within Transcription Factor Bi by Katharina Schulze
Traditional transcription factor binding site analyses focus solely on the nucleotide composition of site despite the fact that more recent studies have shown transcription factors to rely on the DNA structural features within and surrounding their binding sites. In this study a metric of intrinsic DNA flexibility referred to as the TRX scale is used to assess the structural features within functionally annotated binding sites and their up- and downstream flanking regions based on their Shannon information content (IC). Two methods of sequence alignment, center and a novel delta TRX based multiple sequence alignment, are compared. The results show that at least 95% of all up- and downstream flanking regions contained more IC in their structural signature as defined by the TRX scale. Between 23% and 35% (excluding and including bridging phosphate bonds, respectively) of flanking regions also showed significant differences between the sets of confirmed and non-confirmed matches. However, few to no
https://scholarworks.rit.edu/theses/8368/
Laboratory for Computational Molecular Design｜RIKEN Quantitative Biology Center
The Computational Molecular Design Group aims to simulate biomolecular interactions and to design effective molecular regulators using large-scale computer simulations. X-ray crystallography and NMR studies provide a large number of 3D structures of biomolecules, and advances in molecular detection technologies have greatly improved our understandings of intracellular molecular behaviors. To connect molecular behavior with molecular structure and to predict molecular functions, however, require large scale, atomic level molecular simulations. We are therefore focusing on molecular dynamics (MD) and quantum chemistry simulations to study this relationship in large biomolecules. Through collaboration with groups inside and outside QBiC, we are designing novel compounds for various target biomolecules by utilizing our computational techniques. Furthermore, by developing exclusive high-performance computers, we aim to achieve unprecedented long-term MD simulations.. ...
http://www.qbic.riken.jp/english/research/outline/lab-09.html
Computational Chemistry Highlights: May 2012Computational Chemistry Highlights: May 2012
In 2005, Goodman and co-workers introduced the ROBIA (Reaction Outcome By Informatics Analysis) program for predicting the possible products of organic reactions and assessing the kinetic and/or thermodynamic feasibility of product formation. This program combines a series of rules based on typical reactivity patterns of certain organic functional groups with molecular mechanics and/or quantum chemical energy calculations on predicted products and/or transition state structures for possible reactions. Using this program, Goodman and co-workers predicted that (-)-dolabriferol might be formed - both biosynthetically and possibly synthetically - by a retro-Claisen reaction of a polyketide-derived precursor, i.e., they predicted that dolabriferol would likely be one of the major thermodynamic products of such a reaction. Now, Goodman and co-workers describe in ACIE a laboratory synthesis of (-)-dolabriferol that involves just such a (biomimetic) reaction (of a suitably protected precursor). This ...
http://www.compchemhighlights.org/2012/05/
A structural basis for the specificity of protein-protein recognition | Isaac Newton Institute for Mathematical SciencesA structural basis for the specificity of protein-protein recognition | Isaac Newton Institute for Mathematical Sciences
We compare the geometric and physical chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein-protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions, by 188 pairs of monomeric proteins making crystal packing contacts selected to bury more than 800 Å2 of protein surface. A majority of these pairs have two-fold symmetry and form crystal dimers that cannot be distinguished from real dimers on the basis of the interface size or symmetry. Their chemical and amino acid compositions resemble the protein solvent accessible surface, they are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score to assess preferences for the different types of interfaces, and we derive indexes to evaluate the atomic packing, which is less compact at non-specific than ...
http://www.newton.ac.uk/node/971145
Probing large-scale conformational changes and other coupled processes in RNA polymerase, lac repressor, and IHF - DNA...Probing large-scale conformational changes and other coupled processes in RNA polymerase, lac repressor, and IHF - DNA...
Solute effects arise from PREFERENTIAL INTERACTIONS (Timasheff): Solute and water compete for the biopolymer surface Preferential Accumulation of Solute: Solute-Biopolymer interactions more favorable than interactions of both species with water Local concentration of solute higher than bulk Preferential Exclusion of Solute (Preferential Hydration) Local concentration of solute lower than bulk To describe solute distribution: Schellman 1:1 solute: water competitive binding model Our solute partitioning model; partition coefficient K p K p = m 3 loc /m 3 bulk If K p > 1, solute is accumulated; if K p < 1, solute is excluded
http://slideplayer.com/slide/3497933/
Ch431 Lec 14
Lets look at folding in another way: You might guess a protein would fold to lowest free energy conformation. Problem: is there time? (Levinthals Paradox, formulated by Cyrus Levinthal in 1968) Stryer calculation (very conservative): Assume 100 aa residue protein with 3 possible conformations/residue; then get 3100or 5 x 1047 possible conformations. If search at a rate of one structure/10-13sec then get (5 x 1047)(10-13)= 5 x 1034 sec or 1.6 x 1027 years to search (and thus to fold protein). This is greater than the age of our Universe (13.7 x 109 yrs). [Rawn calculation (perhaps more realistic): same but assume 10 conformations, then get 1087sec or 3 x 1080 yrs!]. Obviously from these calculations not searching all possible conformations (or we have the process wrong!), so cannot say protein achieves the lowest global free energy, but rather a local free energy minima. (Like a valley in mountain range: a local energy minima, but not lowest [Marianas trench].) [sketch - note represents ...
http://users.humboldt.edu/rpaselk/C431.F08/C431Notes/C431nLec14.htm
DL ANALYSER - A general analysis tool for DL POLY. CCP5 Software | CCP5 Computer Simulations of Condensed PhasesDL ANALYSER - A general analysis tool for DL POLY. CCP5 Software | CCP5 Computer Simulations of Condensed Phases
The analysis software contains the unique feature whereby it can detect, quantify and annotate the various modes of atomic interactions, without the need of using pictorial or diagrammatic illustrations. This is achieved by making use of the DL_F Notation, implemented within the DL_FIELD program. From such, the DL_ANALYSER Notation for Atomic Interactions, DANAI, has been implemented. It is a natural expression system to annotate detailed, localised atomic interactions. For more details, please refer to the following reference:. C.W. Yong and I.T. Todorov, Molecules (2018), 23, 36 (doi:10.3390/molecules23010036). DL_ANALYSER is supplied to individuals under an academic licence, which is free to academic scientists pursuing scientific research of a non-commercial nature. Please see the web page Registering for the DL_ANALYSER Package for instructions. Commercial organisations interested in acquiring the package should approach Dr. C. W. Yong at Daresbury Laboratory in the first instance. ...
http://www.ccp5.ac.uk/DL_ANALYSER/
Thermodynamic, Energetic, and Topological Properties of Crystal Packing of Pyrazolo[1,5-a] Pyrimidines Governed by Weak...Thermodynamic, Energetic, and Topological Properties of Crystal Packing of Pyrazolo[1,5-a] Pyrimidines Governed by Weak...
A series of pyrazolo[1,5-a] pyrimidines was used as a molecular model in order to understand the crystal packing of compounds with weak electrostatic intermolecular interactions. Additionally, the relationship between the energetic content of intermolecular interactions, the contact surfaces of molecules, and the thermodynamic properties of the crystal was established. The approach, which is based on a supramolecular cluster, shows that for compounds with weak electrostatic intermolecular interactions, the energetic content of the interactions is associated with a large contact surface. The crystal packing of the studied compounds is mainly governed by interactions that involve high interaction energy over a large contact surface. These results show that pi center dot center dot center dot pi interaction may be as responsible as other strong interactions for driving the crystal packing of compounds with weak electrostatic intermolecular interactions. Furthermore, the correlation between ...
https://utd-ir.tdl.org/handle/10735.1/5162
Constrained solution scattering modelling of human antibodies and complement proteins reveals novel biological insights |...Constrained solution scattering modelling of human antibodies and complement proteins reveals novel biological insights |...
Constrained modelling is well suited for determining antibody solution structures and evaluating their flexibility. Monomeric antibodies are composed of two Fab and one Fc fragments joined by two linker peptides called the hinges (Janeway et al. 2005). The hinge conformation comprises the main variable in scattering modelling. The hinge conformation is central to antibody structure and function in all five human antibody classes (IgG, IgA, IgM, IgE and IgD), in which it is the most diverse structural element (figure 4). It can be very short (IgG, IgA) or very long with 64 residues (IgD), or the linker is replaced by an extra pair of domains (IgE, IgM). Very few crystal structures for intact antibodies are known, and only for the IgG class. These crystal structures are obtained using non-physiological buffers in high salt as precipitant, and report a single snapshot view of the two hinge conformations in a single symmetric or asymmetric structure that is frozen by the intermolecular contacts ...
http://rsif.royalsocietypublishing.org/content/6/Suppl_5/S679
The Free Energy Barrier for Arginine Gating Charge Translation Is Altered by Mutations in the Voltage Sensor DomainThe Free Energy Barrier for Arginine Gating Charge Translation Is Altered by Mutations in the Voltage Sensor Domain
The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting pore, thus visiting several intermediate conformations during gating. However, the exact conformational changes are not known in detail. For instance, it has been suggested that there is a local rotation in the helix corresponding to short segments of a 3(10)-helix moving along S4 during opening and closing. Here, we have explored the energetics of the transition between the fully open state (based on the X-ray structure) and the first intermediate state towards channel closing (C-1), modeled from experimental constraints. We show that conformations within 3 angstrom of the X-ray structure are obtained in simulations starting from the C-1 model, and directly observe the previously suggested sliding 3(10)-helix region in S4. Through systematic free ...
http://liu.diva-portal.org/smash/record.jsf?faces-redirect=true&language=en&searchType=SIMPLE&query=&af=%5B%5D&aq=%5B%5B%5D%5D&aq2=%5B%5B%5D%5D&aqe=%5B%5D&pid=diva2%3A572057&noOfRows=50&sortOrder=author_sort_asc&sortOrder2=title_sort_asc&onlyFullText=false&sf=all
Beta Atomic Contacts: Identifying Critical Specific Contacts in Protei by Qian Lu, Chu Hong HOI et al.Beta Atomic Contacts: Identifying Critical Specific Contacts in Protei by Qian Lu, Chu Hong HOI et al.
Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To
http://ink.library.smu.edu.sg/sis_research/2296/
mdrun mpi d.openmpi(1) - gromacs-openmpi - Debian unstable - Debian Manpagesmdrun mpi d.openmpi(1) - gromacs-openmpi - Debian unstable - Debian Manpages
mdrun_mpi is the main computational chemistry engine within GROMACS. Obviously, it performs Molecular Dynamics simulations, but it can also perform Stochastic Dynamics, Energy Minimization, test particle insertion or (re)calculation of energies. Normal mode analysis is another option. In this case mdrun builds a Hessian matrix from single conformation. For usual Normal Modes-like calculations, make sure that the structure provided is properly energy-minimized. The generated matrix can be diagonalized by gmx nmeig. The mdrun program reads the run input file (-s) and distributes the topology over ranks if needed. mdrun produces at least four output files. A single log file (-g) is written. The trajectory file (-o), contains coordinates, velocities and optionally forces. The structure file (-c) contains the coordinates and velocities of the last step. The energy file (-e) contains energies, the temperature, pressure, etc, a lot of these things are also printed in the log file. Optionally ...
https://manpages.debian.org/unstable/gromacs-openmpi/mdrun_mpi_d.openmpi.1.en.html
Assigned NMR backbone resonances of the ligand-binding region domain of the pneumococcal serine-rich repeat protein (PsrP-BR)...Assigned NMR backbone resonances of the ligand-binding region domain of the pneumococcal serine-rich repeat protein (PsrP-BR)...
The pneumococcal serine rich repeat protein (PsrP) is displayed on the surface of Streptococcus pneumoniae with a suggested role in colonization in the human upper respiratory tract. Full-length PsrP is a 4000 residue-long multi-domain protein comprising a positively charged functional binding region (BR) domain for interaction with keratin and extracellular DNA during pneumococcal adhesion and biofilm formation, respectively. The previously determined crystal structure of the BR domain revealed a flat compressed barrel comprising two sides with an extended beta-sheet on one side, and another beta-sheet that is distorted by loops and beta-turns on the other side. Crystallographic B-factors indicated a relatively high mobility of loop regions that were hypothesized to be important for binding. Furthermore, the crystal structure revealed an inter-molecular beta-sheet formed between edge strands of two symmetry-related molecules, which could promote bacterial aggregation during biofilm formation. ...
https://pub.epsilon.slu.se/17792/
Interatomic distance | definition of interatomic distance by Medical dictionaryInteratomic distance | definition of interatomic distance by Medical dictionary
Looking for online definition of interatomic distance in the Medical Dictionary? interatomic distance explanation free. What is interatomic distance? Meaning of interatomic distance medical term. What does interatomic distance mean?
https://medical-dictionary.thefreedictionary.com/interatomic+distance
china c3 iron seal deep groove ball bearing skf 6202-2z c3
China Deep groove ball bearing catalog of Distributor Distributes QIBR Low Noise Deep Groove Ball Bearing 6417 for Large Machinery Long Service Life Deep Groove Ball Bearings 6415 for General Machinery provided by China manufacturer - Shandong XuanYe Precision Machinery Co Ltd page1 QIBR 6212ZZ Deep groove ball bearings - Nodes bearing QIBR 6212ZZ ball bearings deep groove ball bearing Single-Row ZZ: With Two Shielded related articles QIBR deep groove ball bearing cages Related numbers QIBR 6912ZZ bearing 60mm x 85mm x 13mm QIBR 6212-2Z bearing 60mm x 110mm x 22mm QIBR 6212-2Z/C3 bearing 60mm x 110mm x 22mm QIBR 6212 QIBR 6007-Z/C3 QIBR 3206 A/C3 Light Series Ball Bearing Double Row Converging Angle Design ABEC 1 Precision 25 Contact Angle Open Steel Cage C3 Clearance 30mm Bore 62mm OD 15/16 Width 4770 0 pounds Static Load Capacity 6660 00 pounds Dynamic Load Capacity QIBR 71906 CD/P4ATBTB Specifications 1 High precision deep groove ball bearings 2 Deep groove ball Bearing price and size 3 High ...
https://www.whatshap.be/2017_09_10/9964.html
Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data. -...Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data. -...
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
https://www.semanticscholar.org/paper/Probing-the-Structure-and-Dynamics-of-Proteins-by-Allison-Hertig/57319f2d384ea4c1b118dda4db0eab48eb309e53
NTNU Open: Computational Chemistry Study of Solvents for Carbon Dioxide AbsorptionNTNU Open: Computational Chemistry Study of Solvents for Carbon Dioxide Absorption
Absorption with aqueous amine solvents is at present the most viable technology for CO2 capture. While this is a proven technology, efforts are ongoing to improve it in order to make it a more attractive technology for large scale use to reduce CO2 emissions. Finding solvents with better properties is one approach to improving the technology.. In this thesis methods in computational chemistry are used to improve the understanding of the chemistry of CO2 absorption in amine-water systems. The work is also intended to provide models that can be used to predict the performance of new solvents. Such predictive models are intended to facilitate the screening for new solvents.. The main focus of the computational chemistry work has been to model solvent effects. Most of the work has been based on use of quantum mechanical calculations to determine gas phase properties and different models to determine the solvation energy. Most of the solvation energy calculations have been based on molecular ...
https://ntnuopen.ntnu.no/ntnu-xmlui/handle/11250/244514
Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism - Hammes...Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism - Hammes...
wp-content/uploads/2017/10/blank-box.png 0 0 admin /wp-content/uploads/2017/10/blank-box.png admin2015-01-16 20:47:322015-02-17 21:23:51Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism ...
https://www.hammes-schiffer-group.org/quantum-mechanicalmolecular-mechanical-study-of-the-hdv-ribozyme-impact-of-the-catalytic-metal-ion-on-the-mechanism/
3D-QSAR studies of checkpoint kinase 1 inhibitors based on molecular docking and CoMFA3D-QSAR studies of checkpoint kinase 1 inhibitors based on molecular docking and CoMFA
Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on a series of substituted 1,4-dihydroindeno[1,2-c]pyrazoles inhibitors, using molecular docking and comparative molecular field analysis (CoMFA). The docking results from GOLD 3.0.1 provide a reliable conformational alignment scheme for the 3D-QSAR model. Based on the docking conformations and alignments, highly predictive CoMFA model was built with cross-validated q 2 value of 0.534 and non-cross-validated partial least-squares analysis with the optimum components of six showed a conventional r 2 value of 0.911. The predictive ability of this model was validated by the testing set with a conventional r 2 value of 0.812. Based on the docking and CoMFA, we have identified some key features of the 1,4-dihydroindeno[1,2-c]pyrazoles derivatives that are responsible for checkpoint kinase 1 inhibitory activity. The analyses may be used to design more potent 1,4-dihydroindeno[1,2-c]pyrazoles derivatives and ...
https://espace.curtin.edu.au/handle/20.500.11937/25978
Computational Chemistry - Fields of Application | Fields Application | Technology Trends
Fields of Application. The term theoretical chemistry may be defined as a mathematical description of chemistry, whereas computational chemistry is usually used when a mathematical method is sufficiently well developed that it can be automated for implementation on a computer. In theoretical chemistry, chemists, physicists and mathematicians develop algorithms and computer programs to predict atomic and molecular properties and reaction paths for chemical reactions. Computational chemists, in contrast, may simply apply existing computer programs and methodologies to specific chemical questions.. There are two different aspects to computational chemistry:. ...
http://www.primidi.com/computational_chemistry/fields_of_application
Computational chemistry: Solving real-world chemical problems - Organic & Biomolecular Chemistry BlogComputational chemistry: Solving real-world chemical problems - Organic & Biomolecular Chemistry Blog
Computational chemistry is a powerful tool for understanding real-world chemical problems. The gap between experiment and computational models is growing ever smaller. Calculated results for isolated molecules are becoming more relevant and reliable calculations for larger and larger molecular systems are becoming more accessible.. A computational study of enantioselective spiroacetalization catalyzed by phosphoric acids carried out by researchers at the Universidad de Salamanca and Oxford University effectively demonstrates the ability of advanced computational methods to elucidate key and often subtle factors that lead to different reaction outcomes.. The study uses a hybrid quantum mechanics (QM)/molecular mechanics (MM) method which makes computational simulations of large systems feasible by combining an accurate quantum mechanical description of the interesting part of the system (i.e. the catalyst active site) with the computational efficiency of molecular mechanics applied to the ...
http://blogs.rsc.org/ob/2016/05/27/computational-chemistry-solving-real-world-chemical-problems/
Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case | ChemAxonExtracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case | ChemAxon
Abstract. The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD) trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD) and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different ...
https://chemaxon.com/publication/extracting-conformational-ensembles-of-small-molecules-from-molecular-dynamics-simulations-ampicillin-as-a-test-case
Biology | Free Full-Text | Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation | NotesBiology | Free Full-Text | Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation | Notes
The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3Gs catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctds free energy, and we developed a new method that takes into account the distribution of the proteins dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that
http://www.mdpi.com/2079-7737/1/2/245/notes
Robotics: Protein Structure PredictionRobotics: Protein Structure Prediction
The major challenge of ab initio protein structure predictions is the huge conformational space populated by large proteins which has to be sampled in order to find the native structure. Due to the size of the conformational space, the probability of sampling from the vicinity of the native conformation is low. But is it really necessary to consider all possible conformations while searching? Despite having diverse shapes and functions, proteins only populate a tiny part of the space of possible conformations. Our goal is to leverage our knowledge about these populated topologies to guide the search. We strongly believe that using this information during sampling will alleviate many of the problems arising from the size of the conformational space. This in turn should allow us to predict many proteins which are traditionally unsolved by ab initio. Contact: Mahmoud Mabrouk ...
https://www.robotics.tu-berlin.de/menue/research/protein_structure_prediction/parameter/en/minhilfe/?cHash=be29d409bf814844064a1c219f77624c&tx_sibibtex_pi1%5Bsort%5D=journal%3A1
Computational Studies on the Energetics and Dynamics of Biomolecular SystemsComputational Studies on the Energetics and Dynamics of Biomolecular Systems
Computational chemistry offers many avenues to investigate physical phenomena at the molecular level which is usually not totally captured by experiments. Its applications on biological problems present a whole new perspective to living organisms at a micro scale. Folding mechanisms of proteins into their functional forms, assembly formation mechanisms of multiple proteins, signal transduction pathways through a series of proteins and lipids, interactions of proteins and nucleic acids, catalysis pathways of enzymes, and binding principles of small molecules to enzymes belong to a long list of areas to be explored with computational chemistry to make sense of observations made at macroscopic scale.This dissertation features discussions pertaining protein structure, dynamics, and ligand binding. Quantum mechanics and molecular dynamics are employed to gain insights into sample problems in these areas. The first chapter introduces how computational chemistry might aid in the understanding of ...
http://ufdc.ufl.edu/UFE0046515/00001
Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets (Journal Article) |...Periodic boundary conditions for QM/MM calculations: Ewald summation for extended Gaussian basis sets (Journal Article) |...
An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave functions periodic images using ChElPG atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of ...
https://www.osti.gov/scitech/biblio/22253225-periodic-boundary-conditions-qm-mm-calculations-ewald-summation-extended-gaussian-basis-sets
Computational chemistry studies of UV induced processes in human skin - OpenThesis
This thesis presents and uses the techniques of computational chemistry to explore two different processes induced in human skin by ultraviolet light. The first is the transformation of urocanic acid into a immunosuppressing agent, and the other is the enzymatic action of the 8-oxoguanine glycosylase enzyme. The photochemistry of urocanic acid is investigated by time-dependent density functional theory. Vertical absorption spectra of the molecule in different forms and environments is assigned and candidate states for the photochemistry at different wavelengths are identified. Molecular dynamics simulations of urocanic acid in gas phase and aqueous solution reveals considerable flexibility under experimental conditions, particularly for for the cis isomer where competition between intra- and inter-molecular interactions increases flexibility. A model to explain the observed gas phase photochemistry of urocanic acid is developed and it is shown that a reinterpretation in terms of a mixture ...
http://www.openthesis.org/documents/Computational-chemistry-studies-UV-induced-420367.html
DSpace at Jadavpur University: Ab-Initio Protein Structure Prediction using Bacterial Foraging Optimization Algorithm
The protein structure prediction (PSP) problem is concerned with the prediction of native tertiary structure of a protein given its sequence of amino acids. Ab-initio approach to PSP problem assumes that native conformation of protein corresponds to the global minimum free energy state. The potential energy used to evaluate the conformation of a protein is based on different interaction energies. In the present work, potential energy function Chemistry at HARvard Macromolecular Mechanics (CHARMM) has been used to qualitatively assess the conformations. Backbone and side-chain torsion angles are used to represent each conformation. In the present thesis, we have used Bacterial Foraging Optimization Algorithm as a search procedure for exploring the conformational space of the PSP problem. Results obtained indicate that this is another promising way of finding the stable structure of protein ...
http://dspace.jdvu.ac.in/handle/123456789/29107
1pqa - Proteopedia, life in 3D1pqa - Proteopedia, life in 3D
A series of crystal structures of trypsin, containing either an autoproteolytic cleaved peptide fragment or a covalently bound inhibitor, were determined at atomic and ultra-high resolution and subjected to ab initio quantum chemical calculations and multipole refinement. Quantum chemical calculations reproduced the observed active site crystal structure with severe deviations from standard stereochemistry and indicated the protonation state of the catalytic residues. Multipole refinement directly revealed the charge distribution in the active site and proved the validity of the ab initio calculations. The combined results confirmed the catalytic function of the active site residues and the two water molecules acting as the nucleophile and the proton donor. The crystal structures represent snapshots from the reaction pathway, close to a tetrahedral intermediate. The de-acylation of trypsin then occurs in true SN2 fashion. Trypsin revisited: crystallography AT (SUB) atomic resolution and quantum ...
http://proteopedia.org/wiki/index.php/1pqa
Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and...Transient States and Barriers from Molecular Simulations and the Milestoning Theory: Kinetics in Ligand-Protein Recognition and...
Author(s): Tang, Zhiye; Chen, Si-Han; Chang, Chia-En A | Abstract: This study presents a novel computational approach to study molecular recognition and binding kinetics for drug-like compounds dissociating from a flexible protein system. The intermediates and their free energy profile during ligand association and dissociation processes control ligand-protein binding kinetics and bring a more complete picture of ligand-protein binding. The method applied the milestoning theory to extract kinetics and thermodynamics information from running short classical molecular dynamics (MD) simulations for frames from a given dissociation path. High-dimensional ligand-protein motions (3N-6 degrees of freedom) during ligand dissociation were reduced by use of principal component modes for assigning more than 100 milestones, and classical MD runs were allowed to travel multiple milestones to efficiently obtain ensemble distribution of initial structures for MD simulations and estimate the transition time and rate
https://escholarship.org/uc/item/3wc5t57w
Fast and effective protein model refinement using deep graph neural networks | Nature Computational ScienceFast and effective protein model refinement using deep graph neural networks | Nature Computational Science
Protein model refinement is the last step applied to improve the quality of a predicted protein model. Currently, the most successful refinement methods rely on extensive conformational sampling and thus take hours or days to refine even a single protein model. Here, we propose a fast and effective model refinement method that applies graph neural networks (GNNs) to predict a refined inter-atom distance probability distribution from an initial model and then rebuilds three-dimensional models from the predicted distance distribution. Tested on the Critical Assessment of Structure Prediction refinement targets, our method has an accuracy that is comparable to those of two leading human groups (FEIG and BAKER), but runs substantially faster. Our method may refine one protein model within ~11 min on one CPU, whereas BAKER needs ~30 h on 60 CPUs and FEIG needs ~16 h on one GPU. Finally, our study shows that GNN outperforms ResNet (convolutional residual neural networks) for model refinement when very limited
https://www.nature.com/articles/s43588-021-00098-9?error=cookies_not_supported&code=5a874c9e-9cfd-4b8c-8d85-9a6fad654c76
Synthesis and Comparative Molecular Field Analysis (CoMFA) of Symmetric and Nonsymmetric Cyclic Sulfamide HIV-1 Protease...Synthesis and Comparative Molecular Field Analysis (CoMFA) of Symmetric and Nonsymmetric Cyclic Sulfamide HIV-1 Protease...
Close The Infona portal uses cookies, i.e. strings of text saved by a browser on the users device. The portal can access those files and use them to remember the users data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser. ...
https://www.infona.pl/resource/bwmeta1.element.acs-doi-10_1021_jm011105v
Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific...Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific...
In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of ...
http://crdd.osdd.net/open/1645/
Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an...Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an...
Calculations have been performed on the entire Fe(Schiff base) · cdHO system using the QM/MM ONIOM (DFT : AMBER) method implemented in Gaussian 09 [29]. The charges and protonation states of all titrable amino acids were automatically assigned using the interface provided by the UCSF Chimera package [30] with the exception of the iron-chelating histidine His20, which was manually set to be consistent with the coordination rules of the metal. Visual inspection was subsequently performed. The total charge of the system is −8 or −7 depending on the oxidation state of the iron. It can be divided by −10 for the isolated protein and +2 or +3 for the inorganic complex. The QM part in the QM/MM partition has a charge +1 in the Fe(II) species and +2 for the Fe(III) ones.. One of the main objectives of this work is to determine whether the experimental structure corresponds to a plausible electronic structure of the metal centre in a resting state configuration or not. Thus, we are interested in ...
http://rsif.royalsocietypublishing.org/content/11/96/20140090
Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...
The IntFOLD-TS method was developed according to the guiding principle that the model quality assessment (QA) would be the most critical stage for our template-based modeling pipeline. Thus, the IntFOLD-TS method firstly generates numerous alternate models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing QA method-ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD-TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per-residue errors. This important information may help to make the 3D models that are produced by the IntFOLD-TS method more useful for ...
http://onlinelibrary.wiley.com/doi/10.1002/prot.23120/abstract?globalMessage=0
Molecular mechanics simulation of the sliding behavior between nested walls in a multi-walled carbon nanotubeMolecular mechanics simulation of the sliding behavior between nested walls in a multi-walled carbon nanotube
Li, Yuan and Hu, Ning and Yamamoto, Go and Wang, Zhongchang and Hashida, Toshiyuki and Asanuma, Hiroshi and Dong, Chensong and Okabe, Tomonaga and Arai, Masahiro and Fukunaga, Hisao. 2010. Molecular mechanics simulation of the sliding behavior between nested walls in a multi-walled carbon nanotube. Carbon. 48 (10): pp. 2934-2940 ...
https://espace.curtin.edu.au/handle/20.500.11937/19496
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Simple computational chemistry: The practical use of quantum chemistry (my opinion)Simple computational chemistry: The practical use of quantum chemistry (my opinion)
Performing quantum chemistry investigations for groups of experimentalists, I have found that quite often the theoretical and experimental methods give different realities, not intersecting each other. This means that if experimental methods are used, for example, to investigate a mechanism of a chemical reaction, or the dependence of experimentally obtained data on some structural properties of the molecules, these methods often lead to wrong conclusions. The quantum chemistry methods disprove these conclusions, but often do not give an alternative, because, as mentioned above, the quantum chemistry is of quite limited applied use. Maybe in the future these realities will intersect, and then the main method of investigations will be the combination of quantum chemistry with the experimental methods ...
https://simplecompchem.blogspot.com/2015/12/the-practical-use-of-quantum-chemistry.html
Buy 6024zz 6024 2rs 6024 Deep Groove Ball Bearings 6000 seris bearing Price,Size,Weight,Model,Width -Okorder.comBuy 6024zz 6024 2rs 6024 Deep Groove Ball Bearings 6000 seris bearing Price,Size,Weight,Model,Width -Okorder.com
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Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation -...Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation -...
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structur Complex molecular systems: supramolecules, biomolecules and interfaces
http://pubs.rsc.org/en/content/articlelanding/2018/cp/c7cp06355e
Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. - Ecole...Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition. - Ecole...
BACKGROUND: Protein fold recognition usually relies on a statistical model of each fold; each model is constructed from an ensemble of natural sequences belonging to that fold. A complementary strategy may be to employ sequence ensembles produced by computational protein design. Designed sequences can be more diverse than natural sequences, possibly avoiding some limitations of experimental databases. METHODOLOGY/PRINCIPAL FINDINGS: WE EXPLORE THIS STRATEGY FOR FOUR SCOP FAMILIES: Small Kunitz-type inhibitors (SKIs), Interleukin-8 chemokines, PDZ domains, and large Caspase catalytic subunits, represented by 43 structures. An automated procedure is used to redesign the 43 proteins. We use the experimental backbones as fixed templates in the folded state and a molecular mechanics model to compute the interaction energies between sidechain and backbone groups. Calculations are done with the [email protected] volunteer computing platform. A heuristic algorithm is used to scan the sequence and conformational
https://hal-polytechnique.archives-ouvertes.fr/hal-00488174
Laboratory of Computational Chemistry and Drug Design, PKU Shenzhen, China | Institution outputs | Nature IndexLaboratory of Computational Chemistry and Drug Design, PKU Shenzhen, China | Institution outputs | Nature Index
Research outputs, collaborations and relationships for Laboratory of Computational Chemistry and Drug Design, PKU Shenzhen published between 1 December 2018 - 30 November 2019 as tracked by the Nature Index.
https://www.natureindex.com/institution-outputs/china/laboratory-of-computational-chemistry-and-drug-design-pku-shenzhen/57513e3d140ba05e748b4571/Chemistry
RCSB PDB - 3JBP: Cryo-electron microscopy reconstruction of the Plasmodium falciparum 80S ribosome bound to E-tRNARCSB PDB - 3JBP: Cryo-electron microscopy reconstruction of the Plasmodium falciparum 80S ribosome bound to E-tRNA
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
https://www.rcsb.org/structure/3JBP
MADGELAS - Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins | AcronymAtticMADGELAS - Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins | AcronymAttic
How is Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins abbreviated? MADGELAS stands for Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins. MADGELAS is defined as Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins very frequently.
https://www.acronymattic.com/Molecular-description-of-Aggregation%2C-Denaturation%2C-Gelation-And-Surface-activity-of-whey-proteins-
Reaction of formaldehyde with phenols: a computational chemistry study. | TreesearchReaction of formaldehyde with phenols: a computational chemistry study. | Treesearch
Phenolic resins are important adhesives used by the forest products industry. The phenolic compounds in these resins are derived primarily from petrochemical sources. Alternate sources of phenolic compounds include tannins, lignins, biomass pyrolysis products, and coal gasification products. Because of variations in their chemical structures, the reactivities of these phenolic compounds with formaldehyde vary in quite subtle ways. A method is needed for predicting the reactivity of phenolic compounds with formaldehyde in order to allow researchers to efficiently choose those compounds that might make the best candidates for new adhesive systems prior to conducting extensive laboratory trials. Computational chemistry has been used to study the relationship between the reactivity of a number of phenolic compounds with formaldehyde in an aqueous, alkaline system, and charges calculated for reactive sites on the aromatic ring of the phenolic compound. Atomic-charges for each phenolic compound were ...
https://www.fs.usda.gov/treesearch/pubs/6326
Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. - Nuffield...
Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.
https://www.ndm.ox.ac.uk/publications/665269
A Job Submission Portal for Computational Chemistry | Edinburgh Data-Intensive Research
Although some scientists, such as many physicists, may prefer a commandline approach to submitting computational jobs, a majority of scientists want to be shielded from the commandline. A popular approach is to build portals; user community web sites that allow job submissions from the convenience of a web browser. The development of such portals typically takes many months as the developer has to learn how to integrate the various components: a portal system such as GridSphere, a job submission architecture such as Globus, a security system such as the Java CoG Kit, a system for staging input and output files, and so on. In this project, you will design and implement a job submission portal for computational chemistry (http://www.eastchem.ac.uk/). They already have clusters in place and also have access to the Edinburgh Compute Data Facility (http://www.ecdf.ed.ac.uk/). They use grid certificates and rely on Globus for job submissions.. You will _not_ use the conventional approach of ...
http://research.nesc.ac.uk/node/218
Conformational selection by the aIF2 GTPase: a molecular dynamics study of functional pathways. - Ecole polytechniqueConformational selection by the aIF2 GTPase: a molecular dynamics study of functional pathways. - Ecole polytechnique
Archaeal initiation factor 2 (aIF2) is a GTPase involved in protein biosynthesis. In its GTP-bound, ON conformation, it binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, OFF conformation, it dissociates from tRNA. To improve our understanding of the role of each conformational state in the aIF2 life cycle, we start from the state immediately after GTP hydrolysis, ON:GDP:P(i) (where P(i) is inorganic phosphate), and consider the possible next steps on the pathway to the OFF:GDP product. The first possibility is P(i) dissociation, leading to ON:GDP, which could then relax into OFF:GDP. We use molecular dynamics simulations to compute the P(i) dissociation free energy and show that dissociation is highly favorable. The second possibility is conformational relaxation into the OFF state before P(i) dissociation, to form OFF:GDP:P(i). We estimate the corresponding free energy approximately, 2 ± 3.5 kcal/mol, so that this is an uphill or weakly downhill process. A third
https://hal-polytechnique.archives-ouvertes.fr/hal-00488190
BE.442 Molecular Structure of Biological Materials, Fall 2005BE.442 Molecular Structure of Biological Materials, Fall 2005
Basic molecular structural principles of biological materials. Molecular structures of various materials of biological origin, including collagen, silk, bone, protein adhesives, GFP, self-assembling peptides. Molecular design of new biological materials for nanotechnology, biocomputing and regenerative medicine. Graduate students are expected to complete additional coursework. Description from course home page: This course, intended for both graduate and upper level undergraduate students, will focus on understanding of the basic molecular structural principles of biological materials. It will address the molecular structures of various materials of biological origin, such as several types of collagen, silk, spider silk, wool, hair, bones, shells, protein adhesives, GFP, and self-assembling peptides. It will also address molecular design of new biological materials applying the molecular structural principles. The long-term goal of this course is to teach molecular design of new biological ...
https://dspace.mit.edu/handle/1721.1/36885?show=full
Annual Reports in Computational Chemistry, Volume 7 - 1st EditionAnnual Reports in Computational Chemistry, Volume 7 - 1st Edition
Purchase Annual Reports in Computational Chemistry, Volume 7 - 1st Edition. Print Book & E-Book. ISBN 9780444538352, 9780444543028
https://www.elsevier.com/books/annual-reports-in-computational-chemistry/wheeler/978-0-444-53835-2
A single hydrogen bond affects photophysics of chromophores - PCCP BlogA single hydrogen bond affects photophysics of chromophores - PCCP Blog
Green fluorescent protein (GFP) is a luminescent protein with a central chromophore and is used in biological imaging. By modifying the chromophore itself or the protein environment, the photophysical properties can be fine-tuned, yet until recently this has not been well understood. However, Lars Andersen (Aarhus University) and his group have developed a laser-action spectroscopy technique to enable the chromophore to be studied in a vacuum. This has revealed that a single hydrogen bond initiated a 0.5eV shift in the absorption spectrum of the GFP chromophore and highlights the importance of understanding the biophysics of chromophores and how this can help in the development of new colour chromophores.. ...
http://blogs.rsc.org/cp/2015/07/06/a-single-hydrogen-bond-affects-photophysics-of-chromophores/
An n →π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion HoleAn n →π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole
Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1′ positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π∗ interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π∗ orbital and facilitating its hydration. These previously unappreciated interactions entail a form of ...
https://dspace.mit.edu/handle/1721.1/125571
Spectral properties of thermal fluctuations on simple liquid surfaces below shot-noise levels<...
TY - JOUR. T1 - Spectral properties of thermal fluctuations on simple liquid surfaces below shot-noise levels. AU - Aoki, Kenichiro. AU - Mitsui, Takahisa. PY - 2012/7/18. Y1 - 2012/7/18. N2 - We study the spectral properties of thermal fluctuations on simple liquid surfaces, sometimes called ripplons. Analytical properties of the spectral function are investigated and are shown to be composed of regions with simple analytic behavior with respect to the frequency or the wave number. The derived expressions are compared to spectral measurements performed orders of magnitude below shot-noise levels, which is achieved using a novel noise reduction method. The agreement between the theory of thermal surface fluctuations and the experiment is found to be excellent, elucidating the spectral properties of the surface fluctuations. The measurement method requires relatively only a small sample both spatially (few μm) and temporally (∼20s). The method also requires relatively weak light power ...
https://keio.pure.elsevier.com/en/publications/spectral-properties-of-thermal-fluctuations-on-simple-liquid-surf
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo<...
TY - JOUR. T1 - Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. AU - Woods, Chanin T.. AU - Lackey, Lela. AU - Williams, Benfeard. AU - Dokholyan, Nikolay V.. AU - Gotz, David. AU - Laederach, Alain. N1 - Funding Information: This work was supported by the National Institutes of Health (NIH) under grant Nos. HL111527, GM101237, and HG008133 to A.L., grant Nos. R01 GM123238-01, 1R01GM123247, and R01 GM064803-12 to N.V.D., and grant No. 3R01GM080742-08S1 to B.W. L.L. was supported by an American Cancer Society ? Lee National Denim Day Postdoctoral Fellowship, grant No. PF-15-133-01-RMC. Publisher Copyright: © 2017 Biophysical Society Copyright: Copyright 2017 Elsevier B.V., All rights reserved.. PY - 2017/7/25. Y1 - 2017/7/25. N2 - When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular ...
https://pennstate.pure.elsevier.com/en/publications/comparative-visualization-of-the-rna-suboptimal-conformational-en
Atom centered potentials for the description and the design of chemical compounds within density functional theoryAtom centered potentials for the description and the design of chemical compounds within density functional theory
Within the Born-Oppenheimer picture of the electronic Schrödinger equation the external potential due to the nuclei influences the resulting expectation values during the self consistent field procedure. In this thesis, the optimization and the benefit of atom centered potentials for an improved description and design of molecules is studied using density functional theory (DFT). It is shown that atom centered potentials can be used to increase the accuracy of the description of molecular properties as well as to generally explore chemical space rationally for structures which exhibit desired properties. The wide range of possible applications is illustrated by addressing several issues. First, an automated procedure is proposed for the design of optimal link pseudopotentials for quantum mechanics/molecular mechanics calculations. Secondly, it is shown how to tune variationally atom centered potentials within density functional perturbation theory in order to minimize the deviation in electron density
https://infoscience.epfl.ch/record/33724
A Spectral Approach for the Design of Experiments: Design, Analysis and AlgorithmsA Spectral Approach for the Design of Experiments: Design, Analysis and Algorithms
This paper proposes a new approach to construct high quality space-filling sample designs. First, we propose a novel technique to quantify the space-filling property and optimally trade-off uniformity and randomness in sample designs in arbitrary dimensions. Second, we connect the proposed metric (defined in the spatial domain) to the quality metric of the design performance (defined in the spectral domain). This connection serves as an analytic framework for evaluating the qualitative properties of space-filling designs in general. Using the theoretical insights provided by this spatial-spectral analysis, we derive the notion of optimal space-filling designs, which we refer to as space-filling spectral designs. Third, we propose an efficient estimator to evaluate the space-filling properties of sample designs in arbitrary dimensions and use it to develop an optimization framework for generating high quality space-filling designs. Finally, we carry out a detailed performance comparison on two ...
https://jmlr.org/papers/v19/17-735.html
Programming van der Waals interactions with complex symmetries into microparticles using liquid crystallinity | Science AdvancesProgramming van der Waals interactions with complex symmetries into microparticles using liquid crystallinity | Science Advances
In the study reported in this paper, we characterized anisotropic van der Waals interactions programmed into microparticles via control of internal LC ordering by quantifying kinetically controlled colloid adsorption over the surfaces of the LC microparticles. Our experiments and supporting calculations revealed that spatial variation of the van der Waals interactions across the surfaces of the LC microparticles was as large as 20 kBT, a magnitude that is sufficiently large to be useful in engineering the bottom-up assembly of soft materials (18). We note that the LC microparticles used in our experiments were prepared by polymerization of RM257. The polymer network formed by the RM257 prevented lateral motion of probe colloids that adsorbed to the surfaces of the LC microparticles. In contrast, a number of past studies have reported adsorption of colloids onto the surfaces of LC microdroplets with mobile interfaces (23, 30). When the interfaces of the LC microdroplets are mobile, adsorbed ...
https://advances.sciencemag.org/content/6/25/eabb1327.full
IJMS | Free Full-Text | Stability and Folding Behavior Analysis of Zinc-Finger Using Simple Models | NotesIJMS | Free Full-Text | Stability and Folding Behavior Analysis of Zinc-Finger Using Simple Models | Notes
Zinc-fingers play crucial roles in regulating gene expression and mediating protein-protein interactions. In this article, two different proteins (Sp1f2 and FSD-1) are investigated using the Gaussian network model and anisotropy elastic network model. By using these simple coarse-grained methods, we analyze the structural stabilization and establish the unfolding pathway of the two different proteins, in good agreement with related experimental and molecular dynamics simulation data. From the analysis, it is also found that the folding process of the zinc-finger motif is predominated by several factors. Both the zinc ion and C-terminal loop affect the folding pathway of the zinc-finger motif. Knowledge about the stability and folding behavior of zinc-fingers may help in understanding the folding mechanisms of the zinc-finger motif and in designing new zinc-fingers. Meanwhile, these simple coarse-grained analyses can be used as a general and quick method for mechanistic studies of metalloproteins.
http://www.mdpi.com/1422-0067/11/10/4014/notes
Solution structure and dynamics of a de novo designed three-helix bundle protein | PNASSolution structure and dynamics of a de novo designed three-helix bundle protein | PNAS
Protein folding is a complex process involving van der Waals and hydrophobic interactions, electrostatics, and hydrogen bonding networks. One approach to understanding protein folding is to design from scratch a particular protein fold, thoroughly characterize its solution properties, and determine its three-dimensional structure. The field of de novo protein design (1, 2) has experienced some recent exciting successes in the redesign of natural proteins to incorporate novel, functional metal-binding sites (3, 4). Also, the redesign of proteins patterned after the sequence or three-dimensional structural motifs such as the zinc finger (5-8), coiled coils (9), or other small protein domains (10, 11) has progressed quite significantly. Unnatural right-handed coiled coils have been successfully designed (12), and small, marginally stable models for protein secondary (13, 14) and supersecondary structures, including helix-loop-helix (15, 16) and three-stranded β-hairpin motifs (17-20), have been ...
https://www.pnas.org/content/96/10/5486?ijkey=ce1aac8cff12357cd85a88a2d576a41619b257ba&keytype2=tf_ipsecsha
Prediction of the receptor conformation for iGluR2 agonist binding - EmployeesPrediction of the receptor conformation for iGluR2 agonist binding - Employees
TY - JOUR. T1 - Prediction of the receptor conformation for iGluR2 agonist binding. T2 - QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. AU - Sander, Tommy. AU - Liljefors, Tommy. AU - Balle, Thomas. N1 - Keywords: Protein flexibility, molecular docking, normal mode analysis, elastic network model, ensemble generation, iGluR2 receptor, domain closure. PY - 2008. Y1 - 2008. KW - Former Faculty of Pharmaceutical Sciences. U2 - 10.1016/j.jmgm.2007.11.006. DO - 10.1016/j.jmgm.2007.11.006. M3 - Journal article. VL - 26. SP - 1259. EP - 1268. JO - Journal of Molecular Graphics and Modelling. JF - Journal of Molecular Graphics and Modelling. SN - 1093-3263. IS - 8. ER - ...
https://drug.ku.dk/employees/?pure=en%2Fpublications%2Fprediction-of-the-receptor-conformation-for-iglur2-agonist-binding
Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs ...Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs ...
We introduce a new type of knowledge-based potentials for protein structure prediction, called evolutionary potentials, which are derived using a single experimental protein structure and all three-dimensional models of its homologous sequences. The new potentials have been benchmarked against other knowledge-based potentials, resulting in a significant increase in accuracy for model assessment. In contrast to standard knowledge-based potentials, we propose that evolutionary potentials capture key determinants of thermodynamic stability and specific sequence constraints required for fast folding.
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-4-r68
Molecular models of DNAMolecular models of DNA
Molecular modeling of RNA polymerase. Molecular modeling of a bacterial DNA primase template. Molecular modeling of DNA ... Molecular modeling of DNA repair Animated skeletal model of A-DNA. Simplified models of chromatin. Simplified model of ... The DNA model shown (far right) is a space-filling, or CPK, model of the DNA double helix. Animated molecular models, such as ... DNA spacefilling molecular model A model of a designed DNA tetrahedron. 15 m long DNA model, Naturalis Biodiversity Center ...
https://en.wikipedia.org/wiki/Molecular_models_of_DNA
Molecular modelMolecular model
Molecular design software Molecular graphics Molecular modelling Ribbon diagram Software for molecular mechanics modeling Space ... The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their ... "Molecular Models - Tangible Representations of the Abstract". PDB Newsletter. 41: 4-5. [1] history of molecular models Paper ... A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an ...
https://en.wikipedia.org/wiki/Molecular_model
Molecular modellingMolecular modelling
... nanostructures modeling Molecular design software Molecular engineering Molecular graphics Molecular model Molecular modeling ... Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. ... The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include ... Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical mechanics (Newtonian mechanics) ...
https://en.wikipedia.org/wiki/Molecular_modelling
Molecular Modeling DatabaseMolecular Modeling Database
The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and ...
https://en.wikipedia.org/wiki/Molecular_Modeling_Database
Molecular Modelling ToolkitMolecular Modelling Toolkit
... which performs common tasks in molecular modelling. The Molecular Modeling Toolkit is a library that implements common ... Konrad Hinsen, The Molecular Modeling Toolkit: A New Approach to Molecular Simulations, As of 28 April 2011[update], MMTK ... "The Molecular Modeling Toolkit: A New Approach to Molecular Simulations". J. Comput. Chem. 21 (2): 79-85. doi:10.1002/(SICI) ... Molecular modelling software, Molecular dynamics software, Python (programming language) software, All stub articles, ...
https://en.wikipedia.org/wiki/Molecular_Modelling_Toolkit
Molecular modeling on GPUsMolecular modeling on GPUs
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA ... Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics) are ... Molecular modelling, Computational chemistry, Molecular dynamics, Chemistry software, GPGPU). ... 2008). "GPU acceleration of cutoff pair potentials for molecular modeling applications". In CF'08: Proceedings of the 2008 ...
https://en.wikipedia.org/wiki/Molecular_modeling_on_GPUs
Monte Carlo molecular modelingMonte Carlo molecular modeling
... physics List of software for Monte Carlo molecular modeling Software for molecular mechanics modeling Bond fluctuation model ... Monte Carlo molecular modelling is the application of Monte Carlo methods to molecular problems. These problems can also be ... Molecular modelling, Theoretical chemistry, Monte Carlo methods, Stochastic models). ... modelled by the molecular dynamics method. The difference is that this approach relies on equilibrium statistical mechanics ...
https://en.wikipedia.org/wiki/Monte_Carlo_molecular_modeling
Comparison of software for molecular mechanics modelingComparison of software for molecular mechanics modeling
... molecular modeling List of software for nanostructures modeling Molecular design software Molecular dynamics Molecular modeling ... Molecular dynamics software, Molecular modelling software, Science software). ... Resources Short list of Molecular Modeling resources OpenScience Biological Magnetic Resonance Data Bank Materials modelling ... This is a list of computer programs that are predominantly used for molecular mechanics calculations. GPU - GPU accelerated I ...
https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling
List of software for Monte Carlo molecular modelingList of software for Monte Carlo molecular modeling
Molecular modelling software, Monte Carlo molecular modelling software). ... This is a list of computer programs that use Monte Carlo methods for molecular modeling. Abalone classical Hybrid MC BOSS ... software Comparison of software for molecular mechanics modeling Comparison of nucleic acid simulation software Molecular ... Towhee) (16 September 2013). "MCCCS Towhee: a tool for Monte Carlo molecular simulation". Molecular Simulation. 39 (14-15): ...
https://en.wikipedia.org/wiki/List_of_software_for_Monte_Carlo_molecular_modeling
Gaussian network modelGaussian network model
Springs are cross-linked to represent mechanical behavior of the material and bridge molecular dynamics (MD) model and finite ... The Gaussian network model is a minimalist, coarse-grained approach to study biological molecules. In the model, proteins are ... Another model for protein dynamics based on elastic mass-and-spring networks is the Anisotropic Network Model. The Gaussian ... The model uses the harmonic approximation to model interactions. This coarse-grained representation makes the calculations ...
https://en.wikipedia.org/wiki/Gaussian_network_model
Open Knowledgebase of Interatomic ModelsOpen Knowledgebase of Interatomic Models
Molecular Physics. 118 (9-10). van der Giessen, Erik (March 2020). "Roadmap on multiscale materials modeling". Modelling and ... OpenKIM has been directly integrated into various prominent molecular modelling and potential fitting software including LAMMPS ... A key aspect of OpenKIM is that in addition to model parameters, it also stores the complete source code of "portable models" ... ASE, DL_POLY, GULP, and potfit, and is recognized in the molecular modelling community as being a critical step towards ...
https://en.wikipedia.org/wiki/Open_Knowledgebase_of_Interatomic_Models
Solvent modelSolvent model
... in contrast to continuum models. These models generally occur in the application of molecular mechanics (MM) and dynamics (MD) ... These models can make useful contributions when the solvent being modelled can be modelled by a single function i.e. it is not ... Solvation Models (SMx) and the Solvation Model based on Density (SMD) have also seen wide spread use. SMx models (where x is an ... The Polarizable continuum model (PCM) is a commonly used implicit model and has seeded the birth of several variants. The model ...
https://en.wikipedia.org/wiki/Solvent_model
Coarse-grained modelingCoarse-grained modeling
Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of ... Hadley KR, McCabe C (July 2012). "Coarse-Grained Molecular Models of Water: A Review". Molecular Simulation. 38 (8-9): 671-681 ... Coarse-grained models have found practical applications in molecular dynamics simulations. Another case of interest is the ... An example is given by the chemomechanical dynamics of a molecular machine, such as Kinesin. The coarse-grained modeling ...
https://en.wikipedia.org/wiki/Coarse-grained_modeling
Animal models of Parkinsons diseaseAnimal models of Parkinson's disease
"Revisiting the Paraquat-Induced Sporadic Parkinson's Disease-Like Model". Molecular Neurobiology. 56 (2): 1044-1055. doi: ... Parkinson's disease animal models are divided into two categories: neurotoxin models and genetic models. Neurotoxin models ... The pre-formed fibril model was developed as a way to study the propagation of α-synuclein. This model consists of injecting ... A limitation to the pre-formed fibril model is that although it is a widely used model, it lacks overt neurodegeneration. The ...
https://en.wikipedia.org/wiki/Animal_models_of_Parkinson's_disease
Stepwise mutation modelStepwise mutation model
Molecular markers provide only a "sample" of the genetic information in which to compare individuals of populations, and can ... The SMM is distinguished from the Kimura-Crow model, also known as the infinite alleles model (IAM), in that as the population ... The original model assumes that if an allele has a mutation that causes it to change in state, mutations that occur in ... The SMM model takes into account the frequency of mismatches between microsatellite loci, meaning the number of times there are ...
https://en.wikipedia.org/wiki/Stepwise_mutation_model
Experimental models of Alzheimers diseaseExperimental models of Alzheimer's disease
Methods in Molecular Biology. Vol. 1727. New York, NY: Springer. pp. 343-352. doi:10.1007/978-1-4939-7571-6_25. ISBN 978-1-4939 ... Experimental models of Alzheimer's disease are cellular or animal models of Alzheimer's disease. There is a distinction between ... Lecanu L, Papadopoulos V (2013-05-01). "Modeling Alzheimer's disease with non-transgenic rat models". Alzheimer's Research & ... Serneels L, T'Syen D, Perez-Benito L, Theys T, Holt MG, De Strooper B (October 2020). "Modeling the β-secretase cleavage site ...
https://en.wikipedia.org/wiki/Experimental_models_of_Alzheimer's_disease
Carbohydrate-insulin modelCarbohydrate-insulin model
Molecular Metabolism. 32: 27-43. doi:10.1016/j.molmet.2019.11.010. ISSN 2212-8778. PMC 6938849. PMID 32029228. Hall, K. D. ( ... Taubes, Gary (2022). "The energy balance model compared with the carbohydrate-insulin model". The American Journal of Clinical ... The carbohydrate-insulin model (CIM) posits that obesity is caused by excess consumption of carbohydrate, which then disrupts ... It is contrasted with the mainstream energy balance model (EBM), which holds that obesity is caused by a excess in calorie ...
https://en.wikipedia.org/wiki/Carbohydrate–insulin_model
Multi-state modeling of biomoleculesMulti-state modeling of biomolecules
This means that even a model that can account for a vast number of molecular species and reactions is not necessarily ... SRSim is integrated in the LAMMPS molecular dynamics simulator and allows the user to specify the model in BNGL. SRSim allows ... Monod J, Wyman J, Changeux JP (May 1965). "On the nature of allosteric transitions: A plausible model". Journal of Molecular ... Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite ...
https://en.wikipedia.org/wiki/Multi-state_modeling_of_biomolecules
Mouse models of breast cancer metastasisMouse models of breast cancer metastasis
This means models can be generated based upon molecular lesions consistent with the human disease. Metastasis is a process of ... Mice may not be an ideal model for breast cancer. This is mainly due to the lack of precision in many of the models. When ... 2003). Models of Breast Cancer: quo vadis, animal modeling? Breast Cancer Research 6(31), 31-38.doi: 10.1186/bcr723 Pulaski BA ... For a list of other mammary gland specific promoters and mouse models see. MMTV-PyMT is the model of breast cancer metastasis, ...
https://en.wikipedia.org/wiki/Mouse_models_of_breast_cancer_metastasis
Animal model of autismAnimal model of autism
Moy, S (2008). "Advances in behavioral genetics: mouse models of autism". Molecular Psychiatry. 13 (1): 4-26. doi:10.1038/sj.mp ... Klauck, S. M.; Poustka, A. (2006). "Animal models of autism". Drug Discovery Today: Disease Models. 3 (4): 313-318. doi:10.1016 ... Bourgeron, T.; Jamain, S. P.; Granon, S. (2006). "Animal Models of Autism". Transgenic and Knockout Models of Neuropsychiatric ... researchers often focus only on single features of autism when using animal models. One of the more common rodent models is the ...
https://en.wikipedia.org/wiki/Animal_model_of_autism
List of model organismsList of model organisms
Agronomy, Molecular biology) Populus, genus used as a model in forest genetics and woody plant studies. It has a small genome ... Lotus japonicus, model legume used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology) ... Genetics, Molecular biology, Agronomy) Medicago truncatula, model legume, closely related to the common alfalfa. Its rather ... Agronomy, Molecular biology) Mimulus guttatus, model organism used in evolutionary and functional genomes studies. The genus ...
https://en.wikipedia.org/wiki/List_of_model_organisms
Bohr modelBohr model
Svidzinsky, Anatoly A.; Scully, Marlan O.; Herschbach, Dudley R. (23 August 2005). "Bohr's 1913 molecular model revisited". ... The Bohr model is a relatively primitive model of the hydrogen atom, compared to the valence shell atom model. As a theory, it ... It came after the solar system Joseph Larmor model (1897), the solar system Jean Perrin model (1901), the cubical model (1902 ... Niels Bohr proposed a model of the atom and a model of the chemical bond. According to his model for a diatomic molecule, the ...
https://en.wikipedia.org/wiki/Bohr_model
Traumatic brain injury modelingTraumatic brain injury modeling
Li Q, Han X, Wang J (August 2016). "Organotypic Hippocampal Slices as Models for Stroke and Traumatic Brain Injury". Molecular ... in vitro models are the most versatile method, because they facilitate analyzing any aspect of TBI, as long as a model is ... This basic model, however, would give such an estimate so rough that it would most likely prove useless unless it modeled a ... Instead, a mathematical model or method for analysis is chosen and then solved with given information. A basic model is a ...
https://en.wikipedia.org/wiki/Traumatic_brain_injury_modeling
Water modelWater model
... implementations Molecular mechanics Molecular modelling Comparison of software for molecular mechanics modeling Solvent models ... The SPC model is rigid, whilst the flexible SPC model is flexible. In the model of Toukan and Rahman, the O-H stretching is ... The SPC/E model results in a better density and diffusion constant than the SPC model. The TIP3P model implemented in the ... The first model to use this approach was the Bernal-Fowler model published in 1933, which may also be the earliest water model ...
https://en.wikipedia.org/wiki/Water_model
Austin Model 1Austin Model 1
"Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model ... Austin Model 1, or AM1, is a semi-empirical method for the quantum calculation of molecular electronic structure in ... Leach, Andrew R. (2001). Molecular Modelling. Pearson Education Limited. ISBN 0-582-38210-6. v t e (Semiempirical quantum ... the first of a new series of general purpose quantum mechanical molecular models". Tetrahedron. 49 (23): 5003. doi:10.1016/ ...
https://en.wikipedia.org/wiki/Austin_Model_1
Model lipid bilayerModel lipid bilayer
Thus, they are used as mimicries of cell membranes for in vitro studies in molecular and cell biology. Many of the studies of ... A model bilayer can be made with either synthetic or natural lipids. The simplest model systems contain only a single pure ... A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering ... More physiologically relevant model bilayers can be made with mixtures of several synthetic or natural lipids. There are many ...
https://en.wikipedia.org/wiki/Model_lipid_bilayer
Quasispecies modelQuasispecies model
The mutation rate and the general fitness of the molecular sequences and their neighbors is crucial to the formation of a ... Quasispecies models have also been proposed by Jose Fontanari and Emmanuel David Tannenbaum to model the evolution of sexual ... A simple mathematical model for a quasispecies is as follows: let there be S {\displaystyle S} possible sequences and let there ... The quasispecies model was put forward by Manfred Eigen and Peter Schuster based on initial work done by Eigen. When ...
https://en.wikipedia.org/wiki/Quasispecies_model
History of molecular theoryHistory of molecular theory
German chemist August Wilhelm von Hofmann was the first to make stick-and-ball molecular models, which he used in lecture at ... which clearly show both semi-correct molecular geometries, such as a linear water molecule, and correct molecular formulas, ... corresponds to the relationship between respective molecular weights. Hence, relative molecular masses could now be calculated ... In chemistry, the history of molecular theory traces the origins of the concept or idea of the existence of strong chemical ...
https://en.wikipedia.org/wiki/History_of_molecular_theory
ABC model of flower developmentABC model of flower development
Ma, Hong (2005). "Molecular Genetic Analyses of Microsporogenesis and Microgametogenesis in Flowering Plants". Annual Review of ... The ABC model of flower development is a scientific model of the process by which flowering plants produce a pattern of gene ... proposed a modified ABC model in 1993. This model suggests that class B genes are not only expressed in verticils 2 and 3, but ... The latter phase has been modelled using the ABC model, which aims to describe the biological basis of the process from the ...
https://en.wikipedia.org/wiki/ABC_model_of_flower_development
Embedded atom modelEmbedded atom model
These models are particularly appropriate for metallic systems. Embedded-atom methods are widely used in molecular dynamics ... In the original model, by Murray Daw and Mike Baskes, the latter functions represent the electron density. The EAM is related ... In computational chemistry and computational physics, the embedded atom model, embedded-atom method or EAM, is an approximation ... doi:10.1016/0920-2307(93)90001-U. "Pair - EAM". LAMMPS Molecular Dynamics Simulator. Retrieved 2008-10-01. v t e (Chemical ...
https://en.wikipedia.org/wiki/Embedded_atom_model
Paul MischelPaul Mischel
Mischel and colleagues integrated whole genome sequencing, cytogenetics and structural modeling to accurately and globally ... Molecular Cell. 67 (1): 128-138.e7. doi:10.1016/j.molcel.2017.05.030. ISSN 1097-4164. PMC 5521991. PMID 28648777. Guo, Deliang ...
https://en.wikipedia.org/wiki/Paul_Mischel
Locus BiosciencesLocus Biosciences
Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA (March 2015). "Cas9 specifies functional viral ... Molecular Microbiology. 87 (5): 1088-99. doi:10.1111/mmi.12152. PMID 23320564. Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, ... Molecular Biology. 21 (9): 771-7. doi:10.1038/nsmb.2875. PMC 4156918. PMID 25132177. Gasiunas G, Barrangou R, Horvath P, ...
https://en.wikipedia.org/wiki/Locus_Biosciences
Uridine monophosphate synthaseUridine monophosphate synthase
Suchi M, Mizuno H, Kawai Y, Tsuboi T, Sumi S, Okajima K, Hodgson ME, Ogawa H, Wada Y (Mar 1997). "Molecular cloning of the ... Deficiency of the enzyme can be studied in the model organism Caenorhabditis elegans. The rad-6 strain has a premature stop ... Suchi M, Harada N, Tsuboi T, Asai K, Okajima K, Wada Y, Takagi Y (1990). "Molecular cloning of human UMP synthase". Purine and ... Suttle DP, Bugg BY, Winkler JK, Kanalas JJ (Mar 1988). "Molecular cloning and nucleotide sequence for the complete coding ...
https://en.wikipedia.org/wiki/Uridine_monophosphate_synthase
Phage displayPhage display
Endemann H, Model P (July 1995). "Location of filamentous phage minor coat proteins in phage and in infected cells". J. Mol. ... Initial work was done by laboratories at the MRC Laboratory of Molecular Biology (Greg Winter and John McCafferty), the Scripps ... Phage display technology was further developed and improved by groups at the Laboratory of Molecular Biology with Greg Winter ... Journal of Molecular Biology. 254 (3): 392-403. doi:10.1006/jmbi.1995.0626. PMID 7490758. Barbas CF, Hu D, Dunlop N, Sawyer L, ...
https://en.wikipedia.org/wiki/Phage_display
Prostaglandin-endoperoxide synthase 2Prostaglandin-endoperoxide synthase 2
PTGS2 (COX-2) exists as a homodimer, each monomer with a molecular mass of about 70 kDa. The tertiary and quaternary structures ... Lornoxicam not only normalized the expression of cyclooxygenases in both models of PVR, but also neutralized the changes of the ... Studies with human pharmacology and genetics, genetically manipulated rodents, and other animal models and randomized trials ... O'Banion MK (1999). "Cyclooxygenase-2: molecular biology, pharmacology, and neurobiology". Crit Rev Neurobiol. 13 (1): 45-82. ...
https://en.wikipedia.org/wiki/Prostaglandin-endoperoxide_synthase_2
PicovirinaePicovirinae
Lavigne, R.; Seto, D.; Mahadevan, P.; Ackermann, H. W.; Kropinki, A. M. (2008). "Unifying classical and molecular taxonomic ... Replication follows the DNA strand displacement model. DNA-templated transcription is the method of transcription. Bacteria ...
https://en.wikipedia.org/wiki/Picovirinae
Black yeastBlack yeast
In recent years, black fungi such as E. dermatitidis or Hortaea werneckii have attracted increasingly attention as model ... A molecular perspective at a glance". Studies in Mycology. 61: 67-75. doi:10.3114/sim.2008.61.06. PMC 2610308. PMID 19287528. ... Molecular and Cellular Mechanisms". PLOS ONE. 7 (11): e48674. Bibcode:2012PLoSO...748674R. doi:10.1371/journal.pone.0048674. ...
https://en.wikipedia.org/wiki/Black_yeast
Mie scatteringMie scattering
Like Mie model, the extended model can be applied to spheres with a radius close to the wavelength of the incident light. There ... Mie scattering (sometimes referred to as a non-molecular scattering or aerosol particle scattering) takes place in the lower ... The Rayleigh scattering model breaks down when the particle size becomes larger than around 10% of the wavelength of the ... In the case of particles with dimensions greater than this, Mie's scattering model can be used to find the intensity of the ...
https://en.wikipedia.org/wiki/Mie_scattering
PANO1PANO1
Human PANO1 protein has a molecular weight of 22.8 kb and a theoretical, isoelectric point of 12.21. From an analysis of the ... A possible cleavage site was identified between amino acids 33 and 34 as depicted in the PANO1 protein model. As mentioned ...
https://en.wikipedia.org/wiki/PANO1
Gamma-aminobutyric acid receptor subunit gamma-2Gamma-aminobutyric acid receptor subunit gamma-2
... alpha 1 beta 3 gamma 2 receptors determined by molecular modeling". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1565 (1 ...
https://en.wikipedia.org/wiki/Gamma-aminobutyric_acid_receptor_subunit_gamma-2
Proto-oncogene tyrosine-protein kinase SrcProto-oncogene tyrosine-protein kinase Src
... interactive 3D model of the structure of SRC Vega geneview Src Info with links in the Cell Migration Gateway Archived 2014-12- ... Molecular and Cellular Biology. 10 (3): 1000-9. doi:10.1128/mcb.10.3.1000. PMC 360952. PMID 1689455. Zan L, Wu H, Jiang J, Zhao ... This discovery changed the current thinking about cancer from a model wherein cancer is caused by a foreign substance (a viral ... "Detection and enumeration of transformation-defective strains of avian sarcoma virus with molecular hybridization". Virology. ...
https://en.wikipedia.org/wiki/Proto-oncogene_tyrosine-protein_kinase_Src
Baum-Welch algorithmBaum-Welch algorithm
They have since become an important tool in the probabilistic modeling of genomic sequences. A hidden Markov model describes ... Burge, Chris; Karlin, Samuel (1997). "Prediction of Complete Gene Structures in Human Genomic DNA". Journal of Molecular ... Solving this model using Baum-Welch demonstrated the ability to predict the location of CNV breakpoint to approximately 300 bp ... The algorithm and the Hidden Markov models were first described in a series of articles by Baum and his peers at the IDA Center ...
https://en.wikipedia.org/wiki/Baum–Welch_algorithm
Pilling-Bedworth ratioPilling-Bedworth ratio
... atomic or molecular mass n {\displaystyle n} - number of atoms of metal per molecule of the oxide ρ {\displaystyle \rho } - ... The P-B ratio is important when modelling the oxidation of nuclear fuel cladding tubes, which are typically made of Zirconium ...
https://en.wikipedia.org/wiki/Pilling–Bedworth_ratio
Coronavirus nucleocapsid proteinCoronavirus nucleocapsid protein
Masters, Paul S. (2006). "The Molecular Biology of Coronaviruses". Advances in Virus Research. 66: 193-292. doi:10.1016/S0065- ... how we made the SARS-CoV-2 3D model] (in Russian). N+1. Archived from the original on 2021-07-30. Retrieved 30 July 2021. Chang ... Molecular Biology and Evolution. 39: msab292. doi:10.1093/molbev/msab292. ISSN 0737-4038. PMC 8549283. PMID 34638137. Cagliani ... "Inhibition of Beta Interferon Induction by Severe Acute Respiratory Syndrome Coronavirus Suggests a Two-Step Model for ...
https://en.wikipedia.org/wiki/Coronavirus_nucleocapsid_protein
NegritoNegrito
The People of the Bamboo - Age - A Socio-Ecological Model. Edition blurb, 2011. Zell, Reg, John M. Garvan. An Investigation: On ... February 2022). "Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia". Molecular Biology and ...
https://en.wikipedia.org/wiki/Negrito
Methylocella silvestrisMethylocella silvestris
Bordel, Sergio; Crombie, Andrew T.; Muñoz, Raúl; Murrell, J. Colin (2020-07-16). "Genome Scale Metabolic Model of the versatile ... November 2005). "Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2". Molecular ...
https://en.wikipedia.org/wiki/Methylocella_silvestris
Caspase-activated DNaseCaspase-activated DNase
Mukae N, Enari M, Sakahira H, Fukuda Y, Inazawa J, Toh H, Nagata S (August 1998). "Molecular cloning and characterization of ... "Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway ... May 2004). "Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway". Molecular Cell. 14 (4 ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Molecular Systems Biology. 3 (1): 89. ...
https://en.wikipedia.org/wiki/Caspase-activated_DNase
MyxobacteriaMyxobacteria
At a molecular level, initiation of fruiting body development in Myxococcus xanthus is regulated by Pxr sRNA. Myxobacteria such ... Sozinova O, Jiang Y, Kaiser D, Alber M (August 2005). "A three-dimensional model of myxobacterial aggregation by contact- ... They typically travel in swarms (also known as wolf packs), containing many cells kept together by intercellular molecular ... Myxobacteria are used to study the polysaccharide production in gram-negative bacteria like the model Myxococcus xanthus which ...
https://en.wikipedia.org/wiki/Myxobacteria
Prokaryotic DNA replicationProkaryotic DNA replication
Journal of Molecular Biology. 106 (4): 963-81. doi:10.1016/0022-2836(76)90346-6. PMID 789903. Drake JW (1970) The Molecular ... Although it is often studied in the model organism E. coli, other bacteria show many similarities. Replication is bi- ... Bussiere DE, Bastia D (March 1999). "Termination of DNA replication of bacterial and plasmid chromosomes". Molecular ... Journal of Molecular Biology. 31 (3): 519-540. doi:10.1016/0022-2836(68)90425-7. PMID 4866337. Leonard, Alan C.; Grimwade, ...
https://en.wikipedia.org/wiki/Prokaryotic_DNA_replication
Shiladitya DasSarmaShiladitya DasSarma
... (born November 11, 1957) is a molecular biologist well-known for contributions to the biology of halophilic ... "Extreme Halophiles Are Models for Astrobiology" (PDF). Microbe. 2006. "Extreme Microbes » American Scientist". www. ... Indian molecular biologists, Indiana University Bloomington alumni, Massachusetts Institute of Technology School of Science ... He is a researcher and teacher of molecular genetics, genomics, and bioinformatics and mentor of undergraduate, graduate and ...
https://en.wikipedia.org/wiki/Shiladitya_DasSarma
Super 4 (2014 TV series)Super 4 (2014 TV series)
They also felt it offered positive role models: "Friendship and a common goal unite the heroes despite their very different ... the doctor's legs and rejoin the two pieces before they are damaged because the slightest bobo will modify the body's molecular ...
https://en.wikipedia.org/wiki/Super_4_(2014_TV_series)
Arsenic trifluorideArsenic trifluoride
3H2O It has a pyramidal molecular structure in the gas phase which is also present in the solid. In the gas phase the As-F bond ... taking the middle ground in between both models. Pradyot Patnaik. Handbook of Inorganic Chemicals. McGraw-Hill, 2002, ISBN 0-07 ...
https://en.wikipedia.org/wiki/Arsenic_trifluoride
Spectral Sciences IncorporatedSpectral Sciences Incorporated
... chemistry and molecular dynamics, energy management, 3-D and spectral scene modeling, spectroscopy, UV through IR optical ...
https://en.wikipedia.org/wiki/Spectral_Sciences_Incorporated
CKLF-like MARVEL transmembrane domain-containing 5CKLF-like MARVEL transmembrane domain-containing 5
Molecular Medicine Reports. 25 (1). doi:10.3892/mmr.2021.12533. PMC 8628290. PMID 34791506. Xiao Y, Yuan Y, Zhang Y, Li J, Liu ... over expression of CMTM5-v1 in Huh7 human hepatic cells also inhibited the ability of these cells to grow in a mouse model of ...
https://en.wikipedia.org/wiki/CKLF-like_MARVEL_transmembrane_domain-containing_5
Halobacterium salinarumHalobacterium salinarum
H. salinarum is as easy to culture as E. coli and serves as an excellent model system. Methods for gene replacement and ... Graur, Dan; Pupko, Tal (2001-02-15). "The Permian Bacterium that Isn't". Molecular Biology and Evolution. Oxford Journals. 18 ( ... Journal of Molecular Biology. 6: 34-8. doi:10.1016/s0022-2836(63)80079-0. PMID 13964964. Peck, R. F.; Dassarma, S; Krebs, M. P ... Molecular Microbiology. 35 (3): 667-76. doi:10.1046/j.1365-2958.2000.01739.x. PMID 10672188. Brijesh Rajanandam, K S; Siva ...
https://en.wikipedia.org/wiki/Halobacterium_salinarum
Nigel UnwinNigel Unwin
"Molecular structure determination by electron microscopy of unstained crystalline specimens" Journal of Molecular Biology 94: ... "Three-dimensional model of purple membrane obtained by electron microscopy" Nature 257:28-32 Unwin P N T, Henderson R (1975), " ... Peter Nigel Tripp Unwin FRS is a British scientist at the MRC Laboratory of Molecular Biology, where he was Head of the ... In 1988 he returned to the MRC Laboratory of Molecular Biology, taking also a joint appointment at the Scripps Research ...
https://en.wikipedia.org/wiki/Nigel_Unwin
MetabolismMetabolism
Phair RD (December 1997). "Development of kinetic models in the nonlinear world of molecular cell biology". Metabolism. 46 (12 ... Cooper GM (2000). "The Molecular Composition of Cells". The Cell: A Molecular Approach (2nd ed.). Archived from the original on ... These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites ... Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the ...
https://en.wikipedia.org/wiki/Metabolism
Genomic imprintingGenomic imprinting
These models of mapping and identifying imprinting effects include using unordered genotypes to build mapping models. These ... Methods in Molecular Biology. Vol. 2093. New York, NY: Springer US. pp. 173-201. doi:10.1007/978-1-0716-0179-2_13. ISBN 978-1- ... However, our understanding of the molecular mechanisms behind genomic imprinting show that it is the maternal genome that ... Statistical frameworks and mapping models are used to identify imprinting effects on genes and complex traits. Allelic parent- ...
https://en.wikipedia.org/wiki/Genomic_imprinting
Sex determination in SileneSex determination in Silene
Moore, R. C.; Harkess, A. E.; Weingartner, L. A. (2016-07-01). "How to be a seXY plant model: A holistic view of sex-chromosome ... "Patterns of molecular evolution in dioecious and non-dioecious Silene". Journal of Evolutionary Biology. 26 (2): 335-346. doi: ... Kejnovsky, Vyskot (2010). "Silene latifolia : The Classical Model to Study Heteromorphic Sex Chromosomes". Cytogenetic and ... "Silene as a model system in ecology and evolution". Heredity. 103 (1): 5-14. doi:10.1038/hdy.2009.34. ISSN 1365-2540. PMID ...
https://en.wikipedia.org/wiki/Sex_determination_in_Silene
Endless Forms Most Beautiful (book)Endless Forms Most Beautiful (book)
Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom is a 2005 book by the molecular ... using the fruit fly Drosophila as the model organism. He has won the Shaw Scientist Award and the Stephen Jay Gould Prize for ... Sean B. Carroll is a professor of molecular biology and genetics at the University of Wisconsin-Madison. He studies the ... "LCMB Investigators". Laboratory of Cell and Molecular Biology at UW-Madison. Retrieved 14 September 2017. Wade, Nicholas (5 ...
https://en.wikipedia.org/wiki/Endless_Forms_Most_Beautiful_(book)
Browsing by Subject Models, MolecularBrowsing by Subject "Models, Molecular"
JavaScript is disabled for your browser. Some features of this site may not work without it ...
https://extranet.who.int/iris/restricted/browse?authority=Models%2C+Molecular&type=mesh
Molecular Modeling | BSC-CNSMolecular Modeling | BSC-CNS
Molecular recognition is the basis of biological function. Docking is among a number of structural bioinformatics strategies ... As one of our main research lines, we model enzymatic activity addressing not only the atomic (and electronic) detailed ... of computational methodology for the structural and energetic characterization of protein interactions at molecular level. ... trying to understand molecular recognition, both to understand structure to function relationships in macromolecules, and to ...
https://www.bsc.es/ca/research-and-development/research-areas/molecular-modeling
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis | NaturePredictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis | Nature
... models both of the molecular assemblies involved1 and of the functional connections between them. Here we show that such models ... have generated a string of models of molecular machines involved in driving early embryogenesis, and are able to propose ... We assessed the overall predictive value of such molecular machine models by dynamic localization of ten previously ... system-level models are still missing for most developmental processes. The first two cell divisions of Caenorhabditis elegans ...
https://www.nature.com/articles/nature03876?error=cookies_not_supported&code=938ab6c6-e6ff-45e9-bfb8-25c813054283
Molecular Modeling Conferences in 2022/2023/2024Molecular Modeling Conferences in 2022/2023/2024
molecular modeling Conferences 2022/2023/2024 is for the researchers, scientists, scholars, engineers, academic, scientific and ... Molecular Modeling. Molecular Modeling Conferences. Molecular Modeling Conferences is an indexed listing of upcoming meetings, ... Molecular Modelling and Molecular Mechanics Conference, Paris (Feb 06-07, 2023) * ICMMSC 2023: Molecular Modeling Software for ... Molecular Modelling and Molecular Design Conference, London (Feb 16-17, 2023) * ICMMSC 2023: Molecular Modeling Software and ...
https://waset.org/molecular-modeling-conferences
Molecular Modeling | iMechanica
Research area: Thermoelastic Modeling of nano and Contunuum Rods - A Molecular Approach ... molecular and multiscale modeling of cement-based materials. The projects include carrying out bottom-up atomistic and ... with a keen interest in applying this knowledge to molecular modeling of DNA-based nanostructures. The candidate must have ... with a keen interest in applying this knowledge to molecular modeling of DNA-based nanostructures. The candidate must have ...
https://www.imechanica.org/taxonomy/term/4863
Molecular ageing in progeroid syndromes: Hutchinson-Gilford progeria syndrome as a model | SpringerLinkMolecular ageing in progeroid syndromes: Hutchinson-Gilford progeria syndrome as a model | SpringerLink
Molecular ageing in progeroid syndromes: Hutchinson-Gilford progeria syndrome as a model. *Henrique Douglas M Coutinho. 1, ... Molecular ageing in progeroid syndromes: Hutchinson-Gilford progeria syndrome as a model ... A range of molecular and cellular mechanisms are likely to contribute to the diverse phenotypes that are seen in the ... Its main components are lamins A, B1, B2 and C, with molecular weight ranging from 60,000 to 78,000. Lamins A and C are formed ...
https://link.springer.com/article/10.1186/1742-4933-6-4
Center for Molecular Modeling - Faculteit Ingenieurswetenschappen en Architectuur - Universiteit GentCenter for Molecular Modeling - Faculteit Ingenieurswetenschappen en Architectuur - Universiteit Gent
The Center for Molecular Modeling (CMM) extensively uses the supercomputer infrastructure. The above figure shows a snapshot ... Methylation of benzene with methanol in a protonated zeolite, using ab initio molecular dynamics simulations. ... from an ab initio molecular dynamics simulations of the methylation reaction of benzene with methanol. This is one of the key ...
https://www.ugent.be/ea/nl/onderzoek/cti_clusters_research_innovation/cluster2/infrastructure_cl2/cmm
PDF) Using Molecular Simulation to Model High-Resolution Cryo-EM ReconstructionsPDF) Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions
simulated annealing molecular dynamics simulation. Here, we use a higher. weight to bias our model toward the cryo-EM map. For ... Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that ... used molecular dynamics simulation biased by cryo-EM electron density. (MDFF) to produce more accurate models of the ternary ... Atomic model of a small region from human ribosome before flexible fitting by the simulated annealing molecular dynamics (A), ...
https://www.researchgate.net/publication/278907962_Using_Molecular_Simulation_to_Model_High-Resolution_Cryo-EM_Reconstructions
Molecular Models - 3B ScientificMolecular Models - 3B Scientific
Molecular Models, 3B Scientific, Unsaturated Fat (Oleic acid), Set of 3 Carbon Configurations, Sodium Chloride, molymod®-Kit, ...
https://www.3bscientific.com/pl/molecular-models,pg_720.html
Eisco Molecular Model Set Includes 135 pieces:Education Supplies, Quantity: | Fisher ScientificEisco Molecular Model Set Includes 135 pieces:Education Supplies, Quantity: | Fisher Scientific
Shop Eisco™ Molecular Model Set  at ... PCR & Molecular Biology. PCR & Molecular Biology. *Thermal ... Fisher Science Education Molecular Model Set - Enables biochemistry students to build large number of organic molecules. ...
https://www.fishersci.com/shop/products/molecular-model-set-12/S13483
Chapter 36: Haplotype Inference Models and Algorithms - Algorithms in Computational Molecular Biology: Techniques, Approaches...Chapter 36: Haplotype Inference Models and Algorithms - Algorithms in Computational Molecular Biology: Techniques, Approaches...
Selection from Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications [Book] ... CHAPTER 36 HAPLOTYPE INFERENCE MODELS AND ALGORITHMS Ling-Yun Wu 36.1 INTRODUCTION With complete genome sequences for humans ... Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications by Get full access to Algorithms in ... Get Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications now with the OReilly learning ...
https://www.oreilly.com/library/view/algorithms-in-computational/9781118101988/OEBPS/9781118101988_epub_c36_r1.htm
Molecules | Special Issue : Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM)Molecules | Special Issue : Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM)
Special Issue "Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM)". * Special ... Interests: molecular modeling and simulation; theoretical photophysics and photochemistry; time resolved spectroscopy; non- ... Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular Mechanics (QM/MM) ... This article belongs to the Special Issue Multiscale Chemical Modeling and Simulations Using Quantum Mechanics/Molecular ...
https://www.mdpi.com/journal/molecules/special_issues/Quantum_Mechanics_Molecular_Mechanics
Table - Simplified Model to Survey Tuberculosis Transmission in Countries Without Systematic Molecular Epidemiology Programs -...
Simplified Model to Survey Tuberculosis Transmission in Countries Without Systematic Molecular Epidemiology Programs Juan ... Simplified Model to Survey Tuberculosis Transmission in Countries Without Systematic Molecular Epidemiology Programs. ...
https://wwwnc.cdc.gov/eid/article/25/3/18-1593-t1
A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular...A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular...
A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular ... A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular ... A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular ... A Geospatial Modeling Approach to Quantifying the Risk of Exposure to Environmental Chemical Mixtures Via a Common Molecular ...
https://www.niehs.nih.gov/research/resources/articles_journals/recent/pdf_2022/a_geospatial_modeling_approach_to_quantifying_the_risk_of_exposure_to_environmental_chemical_mixtures_via_a_common_molecular_target.cfm
British Library EThOS: Molecular modelling and bioinformatics studies of CDK4 and related proteinsBritish Library EThOS: Molecular modelling and bioinformatics studies of CDK4 and related proteins
Molecular modelling and bioinformatics studies of CDK4 and related proteins Author: Shafiq, Muhammad Imtiaz ISNI: 0000 0004 ... CDK4 homology models were generated based on CDK2 templates. However, after the availability of experimentally determined X-ray ... active form by incorporating the structural information from both CDK4 and CDK2 for its later use in molecular modelling. ... the evolution of CDKs is studied and homology models of CDK4 are generated and used to gain insights into its sequential and ...
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.551800
PDF] SketchBio: a scientists 3D interface for molecular modeling and animation | Semantic ScholarPDF] SketchBio: a scientist's 3D interface for molecular modeling and animation | Semantic Scholar
... and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their ... and spring-based layout that accelerate operations common in the formation of molecular models. BackgroundBecause of the ... a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular ... many scientists hire programmers or animators to create models and animations. This both slows the discovery process and ...
https://www.semanticscholar.org/paper/SketchBio%3A-a-scientist%E2%80%99s-3D-interface-for-molecular-Waldon-Thompson/c499d4a6ab77396ab3f054b4310df8842c76da8a
dr. Alexei Halpin: Two-dimensional spectroscopy of molecular excitons in a model dimer system | Seminars | University of...dr. Alexei Halpin: Two-dimensional spectroscopy of molecular excitons in a model dimer system | Seminars | University of...
Alexei Halpin: Two-dimensional spectroscopy of molecular excitons in a model dimer system ... The physics of molecular excitons has been the subject of many recent studies using two-dimensional electronic spectroscopy ( ... These results, analyzed in the framework of a vibronic exciton model, indicate that the signals observed earlier in ... we present a study on a model dimer comprised of identical chromophores with a well defined electronic coupling strength, such ...
https://www.rug.nl/research/zernike/news/seminars/halpin
Uncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse ModelUncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse Model
An early predictive molecular signature was identified that marked the active profibrotic process before histopathologic ... Uncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse Model Cell Mol ... The aim of this study was to gain insight into the dynamics of key molecular processes involved in NASH and to rank early ... Temporal dynamics of key molecular processes involved in the development of NASH were identified, including lipid metabolism, ...
https://pubmed.ncbi.nlm.nih.gov/29276754/
Multi-modal molecular imaging approaches to detect primary cells in preclinical models - Faraday Discussions (RSC Publishing)Multi-modal molecular imaging approaches to detect primary cells in preclinical models - Faraday Discussions (RSC Publishing)
Here we applied new technologies associated with advances in molecular imaging to demonstrate the feasibility of labeling ... Multi-modal molecular imaging approaches to detect primary cells in preclinical models K. Dhaliwal, L. Alexander, G. Escher, A ... Multi-modal molecular imaging approaches to detect primary cells in preclinical models† ... Here we applied new technologies associated with advances in molecular imaging to demonstrate the feasibility of labeling. ...
https://pubs.rsc.org/en/Content/ArticleLanding/2011/fd/c005410k
Ball & spoke DNA Model - MRC Laboratory of Molecular BiologyBall & spoke DNA Model - MRC Laboratory of Molecular Biology
Ball & spoke DNA Model. Title: Ball & spoke DNA Model. Filename: 00002_5x4_col.jpg. Description: Large ball and spoke model of ... DNA, Francis Crick, James Watson, Models Availability: yes. Source: LMB Visual Aids. Date: Creator: LMB Visual Aids. Copyright ... 2022 MRC Laboratory of Molecular Biology,. Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. 01223 ... MRC Laboratory of Molecular Biology. One of the worlds leading research institutes, our scientists are working to advance ...
https://www2.mrc-lmb.cam.ac.uk/photo-archive/ball-spoke-dna-model/
Jmol Molecular Model: Ethanol and Water
Jmol Models Acetanilide. Acetic Acid. Aniline. Benzene. Ethanol. Ethyl Acetate. Glycerol. Indigo. Mauveine. Phenol. Sodium ... Jmol Molecular Model: Ethanol and Water. Use the links in the navigation bar to select the molecule you wish to display. The ... Chime Models. Chem 104. Chem 185. Chem 221. Kevin Dunn. Electrostatics. Bookstore. Marketplace. ... If you have the Chime plugin installed, you may use the "Chime Models" link in the navigation bar. Chime pages generally load ...
https://cavemanchemistry.com/cgi-bin/jmol.cgi?Ethanol_and_Water
Molecular FlowMolecular Flow
You can simulate molecular flow, such as rarefied gas flows in vacuum systems, in COMSOL Multiphysics®. See examples and gain ... You can simulate molecular flow, such as rarefied gas flows in vacuum systems, in COMSOL Multiphysics®. See examples and gain ... Modeling Beam Neutralization with a Charge Exchange Cell. December 16, 2014. A charge exchange cell refers to an area of high- ... You can model a charge exchange cell to analyze its neutralization efficiency. ...
https://www.comsol.de/blogs/category/fluid-and-heat/molecular-flow/
Finite Element Modelling Of The Resistive Heating Of Disposable Molecular Diagnostics DevicesFinite Element Modelling Of The Resistive Heating Of Disposable Molecular Diagnostics Devices
We present a finite element model for the simulation of the resistive heating of microchannels in disposable molecular ... We present a finite element model for the simulation of the resistive heating of microchannels in disposable molecular ... We demonstrate a finite element model that could reduce design time and save on prototyping costs. The validity of the model is ... The physical parameters of the available resistive heating elements were used in our finite element model, and the results of ...
https://www.witpress.com/elibrary/wit-transactions-on-modelling-and-simulation/59/33325
Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer |...Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer |...
Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer. ... Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer ... Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer ... Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer ...
https://www.biorxiv.org/content/10.1101/2021.08.19.456691v1
PA-07-096: Collaborative Research for Molecular and Genomic Studies of Basic Behavior in Animal Models (R01)PA-07-096: Collaborative Research for Molecular and Genomic Studies of Basic Behavior in Animal Models (R01)
Collaborative Research for Molecular and Genomic Studies of Basic Behavior in Animal Models (R01) PA-07-096. NIGMS ... Title: Collaborative Research for Molecular and Genomic Studies of Basic Behavior in Animal Models (R01). Announcement Type ... The organism should be amenable to state-of-the-art molecular and/or genomic analysis. It may be an established model for some ... There is also a paucity of animal models for many aspects of normal and abnormal human behavior, and some existing models are ...
https://grants.nih.gov/grants/guide/pa-files/PA-07-096.html
Towards exact molecular dynamics simulations with invariant machine-learned modelsTowards exact molecular dynamics simulations with invariant machine-learned models
... which hinders truly predictive modeling of dynamics and function of (bio)molecular systems. Classical potentials often fail to ... Our approach provides the key missing ingredient for achieving spectroscopic accuracy in molecular simulations. ... model. The challenge of constructing conservative force fields is accomplished by learning in a Hilbert space of vector-valued ... and quantum mechanics approach that enables the direct reconstruction of flexible molecular force fields from high-level ab ...
https://depositonce.tu-berlin.de/items/111a8bc8-1ccd-45d9-a202-aaf5e85a19c5
2205.08027] Energy transfer in quantum molecular chain -- two models of inhomogeneity
Title:Energy transfer in quantum molecular chain -- two models of inhomogeneity. Authors:B. A. Tay ... Whereas in the first model all exciton modes are connected, in the second model they are coupled in pairs that are not ... The energy transfer efficiency in the first model is affected by the source power whereas in the second model the efficiency is ... In the first model, the minima of the excitation profile in the site basis occur at the edges of the chain, whereas in the ...
https://jp.arxiv.org/abs/2205.08027
The molecular modelling of calixarene inclusion complexes - DORASThe molecular modelling of calixarene inclusion complexes - DORAS
Chapter 2: The molecular modelling of alkali metal complexes with calixarenes. We have published three papers in this area1. ... Chapter 3: The molecular modelling of the enantioselective complexation of chiral amines by chiral calix[4]arenes. With ... The HyperChem molecular modelling software package has been demonstrated to be a straightforward and computationally ... Fayne, Darren (2001) The molecular modelling of calixarene inclusion complexes. PhD thesis, Dublin City University. ...
https://doras.dcu.ie/18696/
Progress in RNA Modelling : the RNA-Puzzles contest | Research Institute of Molecular Pathology (IMP)Progress in RNA Modelling : the RNA-Puzzles contest | Research Institute of Molecular Pathology (IMP)
Seminars and Events at the Research Institute of Molecular Pathology (IMP) and Vienna Biocenter (VBC). ...
https://www.imp.ac.at/calendar/event/progress-in-rna-modelling-the-rna-puzzles-contest/
A mathematical model explains saturating axon guidance responses to molecular gradients | eLifeA mathematical model explains saturating axon guidance responses to molecular gradients | eLife
Mathematical modelling explains why molecular gradients sometimes cause axons to only turn weakly. ... 1) I am not convinced that the anchor point model is a good model for growth cone turning behavior. There is no evidence that ... There is no true prediction of the model (one that would not have been possible before running the model) that is tested in the ... The authors consistently use the wording predicted by the model to describe an outcome of the anchor point model that fits ...
https://elifesciences.org/articles/12248
BiologyBiochemistrySimulationsMoleculesSimulation2018Spectroscopy2022StructuralPredictiveMammalianMechanismsBiologicalDockingEpidemiologyPathwaysBiologistsChemistryProteinInitioMultiscaleCharacterizationProcessesExperimentalBioinformaticsToggleMethodsPredictQuantumScientistsInteractionsAnalysesApproachSolidsInsightsGeneticStudiesProteinsTargetsPathophysiologyVitroCompoundsHomologySystematic evaluationOrganicDiagnosisMechanismApproachesVivoChapterEthanolPhylogenyExperimentallyCellular and molecularPathologyResearchAtomicMathematicalCrystalsTechniquesBiochemical
Biology9
  • The Laboratory for Computational Biology and Biophysics at MIT ( http://lcbb.mit.edu/ ) is seeking a highly motivated recent PhD graduate with expertise in nonlinear finite element analysis, ideally in the area of beam theory, with a keen interest in applying this knowledge to molecular modeling of DNA-based nanostructures. (imechanica.org)
  • Get full access to Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications and 60K+ other titles, with free 10-day trial of O'Reilly. (oreilly.com)
  • Get Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications now with the O'Reilly learning platform. (oreilly.com)
  • Systems biology pipelines were used for gene set enrichment analysis (GSEA) for pathway discovery, consensus molecular subtyping (CMS), and somatic mutation profiling. (biorxiv.org)
  • The purpose of this funding opportunity announcement (FOA), issued by the National Institute of General Medical Sciences (NIGMS) and the National Institute of Child Health and Human Development (NICHD) , National Institutes of Health (NIH), is to facilitate collaborative research, involving behavioral scientists and investigators with expertise in molecular biology and/or genomics, which addresses questions about basic mechanisms of behavior in animal models. (nih.gov)
  • Principal investigators and their collaborators must have complementary expertise in behavioral analysis and molecular biology/genomics. (nih.gov)
  • Molecular dynamics (MD) simulations constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. (tu-berlin.de)
  • Towbin JA, Vatta M. Molecular biology and the prolonged QT syndromes. (medlineplus.gov)
  • The 1999 NIH Bioengineering Consortium (BECON) "Biomedical Imaging Symposium: Visualizing the Future of Biology and Medicine" identified imaging at the cellular and molecular level as a critical need for goals such as the early detection of disease. (nih.gov)
Biochemistry1
  • The School of Biological Sciences provides PhD and MPhil (research degree) programmes in subjects ranging from basic biochemistry, molecular genetics and cancer research, to agricultural science, marine ecology and the economic evaluation of ecosystem services and food retailing. (qub.ac.uk)
Simulations10
  • Methylation of benzene with methanol in a protonated zeolite, using ab initio molecular dynamics simulations. (ugent.be)
  • The above figure shows a snapshot from an ab initio molecular dynamics simulations of the methylation reaction of benzene with methanol. (ugent.be)
  • The physical parameters of the available resistive heating elements were used in our finite element model, and the results of the simulations compared to experimental data. (witpress.com)
  • However, one of the widely recognized and increasingly pressing issues in MD simulations is the lack of accuracy of underlying classical interatomic potentials, which hinders truly predictive modeling of dynamics and function of (bio)molecular systems. (tu-berlin.de)
  • Our approach provides the key missing ingredient for achieving spectroscopic accuracy in molecular simulations. (tu-berlin.de)
  • New techniques have been introduced for including nuclear quantum effects in molecular simulations at a fraction of the cost of path-integral simulations [11], paving the way for a better understanding of hydrogen bonding and proton transfer in molecular systems. (cecam.org)
  • The structure and dynamics of complex biomolecular structures are studied by molecular dynamics simulations. (boku.ac.at)
  • We present semi-analytic models for cloud dispersal mediated by photoevaporation and by dynamical mass ejection, and show that the predicted net SFE and mass loss efficiencies are consistent with the results of our numerical simulations. (harvard.edu)
  • 2007. Derivation of distributed models of atomic polarizability for molecular Simulations . (ub.edu)
  • The project will combine experimental field and lab work with computer simulations to resolve and assess the stability of model marine food webs. (qub.ac.uk)
Molecules7
  • These models are great ways to show how molecules act without needing very expensive microscopes. (teachersource.com)
  • Experimental terahertz (THz) spectroscopy and molecular modeling were used to investigate the network of non-covalent interactions that serve to connect molecules in the solution-phase and solid-state. (syr.edu)
  • Development and application of QM/classical models to describe the effects of plasmonic nanoparticles on the spectroscopic properties of nearby molecules. (gaussian.com)
  • M.F. Iozzi, B. Mennucci, J. Tomasi, R. Cammi, "Excitation Energy Transfer (EET) between molecules in condensed matter: a novel application of the Polarizable Continuum Model (PCM)", J. Chem. (gaussian.com)
  • The free energy of the gel results from two molecular processes: stretching the network, and mixing the network with the small molecules. (imechanica.org)
  • We assume that the local rearrangement is instantaneous, and model the long-range migration by assuming that the small molecules diffuse inside the gel. (imechanica.org)
  • In molecular signaling, a group of molecules in a cell work together to control one or more cell functions. (mdanderson.org)
Simulation6
  • A user-friendly vision-augmented technique to carry out atomic simulation using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations, and the ease of carrying out molecular dynamics simulation in a more efficient way. (semanticscholar.org)
  • We present a finite element model for the simulation of the resistive heating of microchannels in disposable molecular diagnostics devices by means of various resistive heating elements, and demonstrate the validity of this model through experiments. (witpress.com)
  • In this work, we propose an improved QM/MM-based strategy to determine condensed-phase polarizabilities and we use this approach to optimize a new and simple polarizable four-site water model for classical molecular simulation. (vu.nl)
  • In the field of simulation methodology there has been significant developments in multiscale techniques for modelling crystal growth and habit prediction [9, 10]. (cecam.org)
  • S. Jurinovich, G. Pescitelli, L. Di Bari, B. Mennucci, " A TDDFT/MMPol/PCM model for the simulation of exciton-coupled circular dichroism spectra ", Phys. (gaussian.com)
  • I noticed ' homogeneous model' refers to that the multi fluids will share the flow fields in the simulation, and it's often used together with free surface model. (cfd-online.com)
20183
  • 2018. Sampling molecular conformations and dynamics in a multiuser virtual reality framework . (mgms.org)
  • Two-step self-assembly of a spider silk molecular clamp, Nature Communications (2018). (phys.org)
  • After being a fellow in the programme in 2018, I repeated the experience the following year and have been involved in subsequent projects of the Molecular Modelling and Bioinformatics group until now. (irbbarcelona.org)
Spectroscopy1
  • The physics of molecular excitons has been the subject of many recent studies using two-dimensional electronic spectroscopy (2DES), particularly in the context of light harvesting in photosynthesis. (rug.nl)
20221
Structural6
  • Docking is among a number of structural bioinformatics strategies trying to understand molecular recognition, both to understand structure to function relationships in macromolecules, and to derive tools useful in fields like drug design. (bsc.es)
  • The main focus of our research is the development and optimization for High-Performing-Computing (HPC) of computational methodology for the structural and energetic characterization of protein interactions at molecular level. (bsc.es)
  • In the present work the structural features of the active sites of CDKs are compared, the evolution of CDKs is studied and homology models of CDK4 are generated and used to gain insights into its sequential and structural features. (bl.uk)
  • However, after the availability of experimentally determined X-ray structures of CDK4 in an inactive form, CDK4 models were built in a putative active form by incorporating the structural information from both CDK4 and CDK2 for its later use in molecular modelling. (bl.uk)
  • In addition, exploring the vast conformational and structural flexibility of molecular materials is challenging even for empirical potentials: predicting the stable polymorphic forms of a molecular crystal might require considering thousands of different structures. (cecam.org)
  • Today, it is possible to manufacture artificial spider silk of similar properties as the prototype, but the molecular-level structural details responsible for material properties await to be disclosed. (phys.org)
Predictive4
  • We assessed the overall predictive value of such molecular machine models by dynamic localization of ten previously uncharacterized proteins within the living embryo. (nature.com)
  • An early predictive molecular signature was identified that marked the active profibrotic process before histopathologic fibrosis becomes manifest. (nih.gov)
  • This work introduces the most accurate predictive model of growth cone trajectories to date, and deepens our understanding of axon guidance events both in vitro and in vivo. (elifesciences.org)
  • 2.To develop a predictive model based on clinical-pathologic characteristics in Asian NSCLC patients. (who.int)
Mammalian3
  • Emerging models for the molecular basis of mammalian circadian timing. (escholarship.org)
  • This generalisable approach provides unprecedented temporal control over the dose of endogenous proteins in mouse models, with implications for studying essential biological pathways and modelling drug activity in mammalian tissues. (elifesciences.org)
  • In mammalian cell based models of both polyglutamine and polyalanine diseases, the mutant proteins are much more prone to aggregate formation than their wild-type counterparts and cause significantly more cell death. (bmj.com)
Mechanisms5
  • This situation has prompted a search for agents that cause tumor cell death via molecular mechanisms independent of p53. (aspetjournals.org)
  • Defining these detailed mechanisms will provide a foundation for understanding the molecular basis of circadian timing and help to establish new platforms for the discovery of therapeutics to manipulate the clock. (escholarship.org)
  • Ultimately,' he adds, 'better knowledge of molecular mechanisms in infection may suggest strategies to interrupt the viral life cycle and treat infections. (infectioncontroltoday.com)
  • Denic also studies the molecular mechanisms of age-related deterioration in budding yeast. (harvard.edu)
  • We utilise complex models (3D, co-culture, new matrices) to unravel the inricate mechanisms underpinning immune responses to advanced therapeutics. (liverpool.ac.uk)
Biological6
  • Molecular recognition is the basis of biological function. (bsc.es)
  • One of the world's leading research institutes, our scientists are working to advance understanding of biological processes at the molecular level - providing the knowledge needed to solve key problems in human health. (cam.ac.uk)
  • We used an in vitro model to investigate the early biological effects of TNFa and IFNgamma on oxidant production by alveolar macrophages (AM). We used chemiluminescence (CL) as an indirect method to measure oxygen radical generation. (cdc.gov)
  • The study team, formerly based at the Salk Institute for Biological Studies in La Jolla, Calif., published their current findings online March 8 in Molecular Cell. (infectioncontroltoday.com)
  • Many of the leukemia terms have undergone name changes as immunophenotypic and molecular biological techniques have made diagnosis more precise. (bvs.br)
  • 7 These NHPs were cynomolgus macaques used for preclinical research, drug development, disease modelling, experimental infections, and biological production, with breeders being collected from wildlife trapping areas mostly in southern Philippines. (who.int)
Docking4
  • Analyze lysosomotropic agents and their action on COVID-19 targets using the molecular docking technique. (bvsalud.org)
  • Molecular docking analyses of these lysosomotropic agents were performed, namely of fluoxetine, imipramine, chloroquine, verapamil, tamoxifen, amitriptyline, and chlorpromazine against important targets for the pathogenesis of SARS-CoV-2. (bvsalud.org)
  • Molecular Docking. (bvsalud.org)
  • aAnalisar agentes lisossomotrópicos e sua ação em alvos de COVID-19 usando a técnica de docking molecular. (bvsalud.org)
Epidemiology1
  • 1.To evaluate the molecular epidemiology of NSCLC in Asia via comprehensive, prospective molecular profiling of lung cancer specimens â? (who.int)
Pathways5
  • The first goal is to detect and quantify at the molecular and cellular level the cellular pathways that regulate heart, lung and blood function, and the abnormalities in these pathways occurring in heart, lung, blood and sleep disorders. (nih.gov)
  • Molecular imaging is a growing research area aimed at developing and testing novel tools, reagents, and methods to image specific molecular pathways in vivo, particularly those that are key targets in disease processes. (nih.gov)
  • Research Scope The emerging field of molecular imaging uses novel reagents and methods to image specific cellular and molecular pathways in vivo, particularly those that are key targets in disease processes. (nih.gov)
  • 10, 11 In such models, aggregate formation and cell death can be reduced by overexpressing yeast and bacteria derived chaperones that do not appear to protect against some other cell death pathways. (bmj.com)
  • Moon shots investigators have also identified faulty molecular signaling pathways that lead to drug resistance in some MDS patients. (mdanderson.org)
Biologists1
  • Alberts, B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. (nature.com)
Chemistry1
  • ChemDoodle 3D is a powerhouse for working with chemistry in 3D with industry leading molecular modeling tools and best-in-class graphics. (chemdoodle.com)
Protein4
  • Computer generated molecular model of an HIV protein. (scienceimage.csiro.au)
  • After having reliable conformations of them, we build glycosylated proteins by modeling glycan structures onto available deglycosylated protein structures with different techniques in the absence of any experimental data. (boku.ac.at)
  • Scientists from the University of Würzburg discovered new molecular details of self-assembly of a spider silk fibre protein. (phys.org)
  • The molecular interaction between hemoglobin (HHb), the major human heme protein, and the acridine dyes acridine orange (AO) and 9-aminoacridine (9AA) was studied by various spectroscopic, calorimetric and molecular modeling techniques. (jascoinc.com)
Initio1
  • In this thesis, we develop a combined machine learning (ML) and quantum mechanics approach that enables the direct reconstruction of flexible molecular force fields from high-level ab initio calculations. (tu-berlin.de)
Multiscale1
  • Ph.D and postdoctoral associate positions are available at Rice University i n the broad area of atomistic, molecular and multiscale modeling of cement-based materials. (imechanica.org)
Characterization3
  • Our study incorporated a detailed molecular characterization of rhesus CRC for cross-comparison with human MMRd CRC. (biorxiv.org)
  • IMSEAR at SEARO: Molecular characterization and modeling of secondary structure of 16S rRNA from aeromonas veronii. (who.int)
  • Molecular imaging can be broadly defined as the in vivo characterization and measurement of biologic processes at the cellular and molecular level. (nih.gov)
Processes7
  • Although numerous fundamental aspects of development have been uncovered through the study of individual genes and proteins, system-level models are still missing for most developmental processes. (nature.com)
  • The aim of this study was to gain insight into the dynamics of key molecular processes involved in NASH and to rank early markers for hepatic fibrosis. (nih.gov)
  • Temporal dynamics of key molecular processes involved in the development of NASH were identified, including lipid metabolism, inflammation, oxidative stress, and fibrosis. (nih.gov)
  • This class of models is very common, and can be used to describe many astrophysical processes, including the distribution of protostars in molecular clouds. (u-strasbg.fr)
  • Development and application of QM methods to model excitonic processes in supramolecular systems in condensed phase. (gaussian.com)
  • This initiative seeks to take advantage of the rapid advances that have taken place in imaging technology, allowing normal and pathological processes to be studied in vivo at the molecular and cellular level. (nih.gov)
  • His lab is applying new gene editing and control technologies, such as CRISPR/Cas9, to model these disease processes. (harvard.edu)
Experimental4
  • have built a mathematical model that accounts for the way that nerve fibres respond to chemical gradients, and showed that the model closely matched new experimental data on the growth of nerve fibres from the rat brain. (elifesciences.org)
  • Synergistic, combined theoretical and experimental studies of structure and dynamics in molecular systems have also flourished in the past decade [6]. (cecam.org)
  • Molecular modeling was utilized to predict the structure and vibrations of the samples and guide the analysis of the experimental data. (syr.edu)
  • Review and update of ultrasonic vocalization in animals: Correlation with autism spectrum disorder experimental models? (bvsalud.org)
Bioinformatics1
  • Through the Maths4Life Programme, last July I joined the Molecular Modelling and Bioinformatics group led by Dr. Modesto Orozco at IRB. (irbbarcelona.org)
Toggle1
  • So my question is that once I didn't choose free surface model, does it mean I needn't toggle the 'homogeneous model' option please? (cfd-online.com)
Methods8
  • Molecular materials are of great fundamental and applied importance in science and industry and provide fertile ground for the continuing development of theoretical methods. (cecam.org)
  • However, there are a number of challenges in applying such methods to molecular systems. (cecam.org)
  • Methods: For animal studies, a well-established model of mouse intranasal inhalation was employed. (cdc.gov)
  • The need for the development of improved methods for molecular and cellular imaging and for cell tracking was identified at several NIH-sponsored workshops and meetings. (nih.gov)
  • The prescreening methods developed in this study performed better than the screening score model that had been developed previously and may be more effective method for prediabetes screening. (hindawi.com)
  • In this study, we aimed to develop and validate models to predict prediabetes using artificial neural network (ANN) and support vector machine (SVM) methods, which could be effective as simple and accurate screening tools. (hindawi.com)
  • The UBC Centre for Molecular Medicine and Therapeutics based at the BC Children's Hospital Research Institute is home to a highly collaborative community of scientists connected by a common commitment to use leading edge molecular methods to advance development of therapeutics for human disease. (ubc.ca)
  • Supported by underpinning technological expertise in cutting edge molecular, genomic, transcriptomic/proteomic and metabolomic methods, the goal of the theme is to transform Agri-Food systems so that they benefit both human nutrition and health while simultaneously reducing the greenhouse gases emissions from livestock production systems, protecting ecological resources, supporting livelihoods and affordable foods, and upholding social, cultural, and ethical values. (qub.ac.uk)
Predict3
  • s model can now be used to predict nerve fibre responses in many other situations, and could help researchers to understand more about how the brain becomes wired up during development. (elifesciences.org)
  • We have used molecular modeling to predict CO 2 adsorption in a variety of MOFs under conditions relevant for carbon capture. (northwestern.edu)
  • Oyekola Oyekole (Applied Computational Mathematics and Statistics) impressed with his work on the use of mathematical models to more accurately predict the likelihood that a cardio vascular aneurysm may rupture. (nd.edu)
Quantum4
  • These results, analyzed in the framework of a vibronic exciton model, indicate that the signals observed earlier in photosynthetic proteins likely reflect vibrational motion in isolated pigments, and not delocalized quantum coherence. (rug.nl)
  • Using conservation of energy -- a fundamental property of closed classical and quantum mechanical systems -- we derive an efficient gradient-domain machine learning (GDML) model. (tu-berlin.de)
  • By fitting electrostatic, polarization and dispersion properties of our water model based on quantum and/or combined QM/MM calculations, only a single model parameter (describing exchange repulsion) is left for empirical calibration. (vu.nl)
  • View atomic orbital models based on quantum numbers with the Orbitals widget. (chemdoodle.com)
Scientists2
  • BackgroundBecause of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. (semanticscholar.org)
  • Computational approaches to molecular-materials design can enable scientists to explore the properties of materials in silico, identifying key properties of interest before the costly process of obtaining the material in a laboratory. (cecam.org)
Interactions5
  • With reference to the enantioselective complexation studies we have shown that by using molecular modelling software, an insight can be gained into the interactions that occur on complexation of chiral amines by chiral calixarenes. (dcu.ie)
  • Understanding how atomic-level interactions, structure, and dynamics in molecular materials dictate such macroscopic properties is essential for rational material design. (cecam.org)
  • These improvements have gone hand-in-hand with a deeper understanding of the role of non-covalent interactions, particularly van der Waals interactions [3-5], in governing cohesive properties of molecular crystals and supramolecular assemblies. (cecam.org)
  • This animation shows the molecular interactions involved in the negative feedback loop responsible for circadian rhythms in mammals. (dnatube.com)
  • Molecular modeling studies specified the binding site and the non-covalent interactions involved in the association. (jascoinc.com)
Analyses2
  • For the purpose of reproducibility, we here provide key datasets supporting the analyses of the paper 'Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms' by Ortiz-Sepulveda et al. (datadryad.org)
  • Knowledge of R and statistics, marine invertebrate identification, laboratory based molecular analyses, experience of running experiments. (qub.ac.uk)
Approach5
  • A data-integrative approach enabled identification of the active fibrotic process preceding histopathologic detection using a novel molecular fibrosis signature. (nih.gov)
  • The resulting model performs well in describing relevant pure-liquid thermodynamic and transport properties, which illustrates the merit of our approach to minimize the number of free variables in our model. (vu.nl)
  • S. Caprasecca, C. Curutchet, B. Mennucci, "Toward a unified modeling of environment and bridge-mediated contributions to electronic energy transfer: a fully polarizable QM/MM/PCM approach", J. Chem. (gaussian.com)
  • which approach do you refer to , the passive scalar in multicomponent model? (cfd-online.com)
  • Your first line is correct - if the mixing is on the molecular level then a multiphase approach is not appropriate. (cfd-online.com)
Solids2
  • An application of cell theory to molecular models of n-alkane solids" by AP Malanoski, C Vega et al. (umass.edu)
  • These periodic calculations include the relevant molecular environment found in solids which isolated-molecule calculations can not provide. (syr.edu)
Insights1
  • While epidemiological data are available for the dose and dose -rate effectiveness factor (DDREF) for human populations , animal models have contributed significantly to providing quantitative data with mechanistic insights. (bvsalud.org)
Genetic5
  • The objective of this present work was to carry out a literature review of the molecular traits and clinical features of Hutchinson-Gilford progeria syndrome (HGPS), in a search based on mutations in the genes involved with this genetic disease. (springer.com)
  • In this scenario, the zebrafish has arisen as a promising animal model to progress further due to its unique characteristics, such as transparency, ease of genetic manipulation, ethical and economic advantages and also conservation of the major brain regions and blood-brain-barrier (BBB) which are similar to a human structure. (usc.es)
  • A few papers described in this review, using genetic and xenotransplantation zebrafish models have been used to study GBM as well as to test the anti-tumoral efficacy of new drugs, their ability to interact with target cells, modulate the tumor microenvironment, cross the BBB and/or their toxicity. (usc.es)
  • Genetic and transgenic studies are consistent with a model where expanded polyglutamines cause disease by conferring a novel toxic function on the disease proteins. (bmj.com)
  • 2001), but also as phenotypic information to identify affected sibpairs for molecular genetic studies as described in Table 1. (helsinki.fi)
Studies5
  • Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms. (datadryad.org)
  • Data from 450 patients with centrally diagnosed LGGs recruited into 2 large studies conducted by North American cooperative groups were used to validate the models. (eur.nl)
  • These studies will be performed in a rat model exposed to WTC dusts obtained within 72 hr after the buildings collapsed, using exposures that mimic exposures and dust levels faced by FR. (cdc.gov)
  • Regarding animal models in ASD, many studies focus on gene expression, cortical neuronal migration and cell maturation, and neural network deficits. (bvsalud.org)
  • The object of our study aimed to review and to correlate genes involved in ASD and those related to ultrasonic communication in animal model studies of language-based social behavior at the PubMed database. (bvsalud.org)
Proteins2
  • Embryonic localization patterns of GFP-tagged fusion proteins analysed by time-lapse microscopy are largely consistent with model predictions. (nature.com)
  • The determination of the exact molecular structure of glycosylated proteins is often a challenge due to the inherent flexible nature of glycan units. (boku.ac.at)
Targets4
  • Molecular gradients provide critical signals to guide growth cones, which are the motile tips of developing axons, to their targets. (elifesciences.org)
  • Axon guidance, where axons grow and navigate to their targets, occurs primarily via the sensing of molecular cues in the environment. (elifesciences.org)
  • Combined, these data verify the p53-independence of cell death caused by inhibitors of the proteasome pathway and support the proposition that the ubiquitin-dependent proteasome pathway may contain molecular targets suitable for antineoplastic drug discovery. (aspetjournals.org)
  • Viral E3 Ubiquitin Ligase-Mediated Degradation of a Cellular E3: Viral Mimicry of a Cellular Phosphorylation Mark Targets the RNF8 FHA Domain,' Molecular Cell, published online March 8, 2012, to appear in print, April 13, 2012. (infectioncontroltoday.com)
Pathophysiology2
  • Molecular Pathophysiology of Congenital Long QT Syndrome. (medlineplus.gov)
  • Here we will give a brief overview of the roles of IgE in allergic pathophysiology, and the molecular and cellular factors that ultimately regulate IgE production and Th2 expansion. (jci.org)
Vitro4
  • However, in vitro, growth cones trace highly stochastic trajectories, and exactly how molecular gradients bias their movement is unclear. (elifesciences.org)
  • This model provides a mathematical explanation for why average axon turning angles in gradients in vitro saturate very rapidly with time at relatively small values. (elifesciences.org)
  • Our recent investigations with electrophilic prostaglandins enabled us to devise a pharmacophore and mechanism of action hypothesis relevant to this problem: a cross-conjugated α,β-unsaturated dienone with two sterically accessible electrophilic β-carbons is a molecular determinant that confers activity among this class of ubiquitin isopeptidases inhibitors, and that inhibitors of ubiquitin isopeptidases cause cell death in vitro independently of p53. (aspetjournals.org)
  • Relating in vitro to in vivo exposures with physiologically based tissue dosimetry and tissue response models. (cdc.gov)
Compounds2
  • Molymod Molecular Model Sets demonstrate chemical compounds in three dimensions. (teachersource.com)
  • Molecular aspects of monooxygenases and bioactivation of toxic compounds. (cdc.gov)
Homology2
  • CDK4 homology models were generated based on CDK2 templates. (bl.uk)
  • The result indicates the accurate molecular identification of A. veronii and its phylogeny shows the high degree of homology with diverse source of other strains. (who.int)
Systematic evaluation2
  • Bae, YS, Wilmer, CE, Yazaydin, AO & Snurr, RQ 2011, ' Molecular modeling and systematic evaluation of metal-organic frameworks for CO 2 capture ', ACS National Meeting Book of Abstracts . (northwestern.edu)
  • We developed two models to screen for prediabetes using an artificial neural network (ANN) and support vector machine (SVM) and performed a systematic evaluation of the models using internal and external validation. (hindawi.com)
Organic2
  • A new model has revealed how tiny tweaks to the molecular shapes in non-fullerene acceptors can improve the performance of organic solar cells. (materialstoday.com)
  • The applications of molecular materials are wide, ranging from pharmaceuticals to molecular sensors, hybrid organic-inorganic interfaces, as well as energy capture using dye-sensitised solar cells. (cecam.org)
Diagnosis1
  • The ability to obtain molecular information in vivo would help to understand the abnormalities underlying cardiovascular, pulmonary, and blood diseases, would have profound impact on the diagnosis of these conditions, and could provide rapid and efficient assessment of treatment effectiveness. (nih.gov)
Mechanism1
  • As one of our main research lines, we model enzymatic activity addressing not only the atomic (and electronic) detailed mechanism but also suggesting mutations for changes in activity, substrate specificity, etc. (bsc.es)
Approaches2
  • The findings from this study support the use of rhesus macaques as the preferred animal model to study carcinogenesis, develop immunotherapies and vaccines, and implement chemoprevention approaches pertinent to sporadic MSI-H and LS CRC in humans. (biorxiv.org)
  • While DFT can provide reasonable molecular geometries it suffers from severe problems in predicting electronic properties, which calls for much more expensive many-body approaches. (cecam.org)
Vivo2
  • The availability of these basic science tools enhances the capacity of molecular imaging to address basic biologic questions in vivo and to do this in a high-throughput fashion. (nih.gov)
  • 11, 15 Members of the HSP70 and HSP40 family members are recruited to polyQ inclusions in vivo and in cell models. (bmj.com)
Chapter2
  • Chapter 2: The molecular modelling of alkali metal complexes with calixarenes. (dcu.ie)
  • Chapter 3: The molecular modelling of the enantioselective complexation of chiral amines by chiral calix[4]arenes. (dcu.ie)
Ethanol1
  • Aim: To evaluate the long-term bond strength, degree of conversion and resistance to degradation in ethanol of HEMA-containing and HEMA-free model adhesive resins of a three-step etch-andrinse adhesive system. (bvsalud.org)
Phylogeny1
  • Phylogeny -- Molecular aspects. (amnh.org)
Experimentally1
  • Designing, synthesising, and experimentally isolating and characterising molecular materials is very costly and time consuming. (cecam.org)
Cellular and molecular2
  • The production of IgE is tightly regulated and involves a complex network of cellular and molecular signals. (jci.org)
  • Learning details of how cells respond to viruses helps us to understand key cellular machinery better,' says study leader Matthew D. Weitzman, PhD, of the Center for Cellular and Molecular Therapeutics at The Children's Hospital of Philadelphia. (infectioncontroltoday.com)
Pathology4
  • New models in patients with LGGs diagnosed by central pathology revieware needed. (eur.nl)
  • Datafrom339EORTCpatients withLGGsdiagnosed by central pathology reviewwere used to develop newprognostic models for progression-free survival (PFS) and overall survival (OS). (eur.nl)
  • Wehave developed new prognostic models in a more homogeneous LGG population diagnosed by central pathology review. (eur.nl)
  • This population better fits with modern practice, where patients are enrolled in clinical trials based on central or panel pathology review.We could validate the models in a large, external, and independent dataset. (eur.nl)
Research4
  • For several decades, basic research on acquired and inherited retinal degeneration was substantially based on a variety of animal models, most of them originating from spontaneous mutations, others induced by damaging external agents. (bmj.com)
  • With all of these potential applications, the design and control of molecular materials is one of the grand challenges of physical and chemical research. (cecam.org)
  • While there has been limited use of imaging techniques that may be defined as "molecular" for imaging heart, lung, and blood,(e.g., imaging with monoclonal antibodies or receptor imaging with nuclear techniques), it is only recently that needed adjunct basic research tools have become routinely available. (nih.gov)
  • Animal models in research. (amnh.org)
Atomic1
  • R. Cammi, B. Mennucci, J. Tomasi, "Nuclear Magnetic Shieldings in Solution: Gauge Invariant Atomic Orbital Calculation using the Polarizable Continuum Model," J. Chem. (gaussian.com)
Mathematical1
  • Here, we introduce a mathematical model based on persistence, bias, and noise to describe this behaviour, constrained directly by measurements of the detailed statistics of growth cone movements in both attractive and repulsive gradients in a microfluidic device. (elifesciences.org)
Crystals1
  • Molecular Crystals and Liquid Crystals , 509. (strath.ac.uk)
Techniques3
  • Participation of experimentalists interested in application molecular modeling techniques is encouraged. (materialstoday.com)
  • Development of new molecular probes for conventional imaging techniques such as MRI and ultrasound, and application of new technologies such as optical imaging show great promise, but their use in the cardiovascular, pulmonary, and hematopoietic systems is still limited. (nih.gov)
  • The need for improved molecular and cellular imaging techniques was a common thread running through recommendations from several of the subgroups of the January 2003 NHLBI Spark II Conference ( http://www.nhlbi.nih.gov/funding/fromdir/spark2web.htm ). (nih.gov)
Biochemical1
  • obtain biochemical/molecular clues to the CV/neurologic problems of exposed FR. (cdc.gov)
Browsing by Subject Models, Molecular
Browsing by Subject "Models, Molecular" (extranet.who.int)
Substrate recognition and transport behavior analyses of amino acid antiporter with coarse-grained models - Molecular...
Substrate recognition and transport behavior analyses of amino acid antiporter with coarse-grained models - Molecular... (pubs.rsc.org)
National Plan for Reliable Tuberculosis Laboratory Services Using a Systems Approach
National Plan for Reliable Tuberculosis Laboratory Services Using a Systems Approach (cdc.gov)
The let-7-Imp axis regulates ageing of the Drosophila testis stem-cell niche | Nature
The let-7-Imp axis regulates ageing of the Drosophila testis stem-cell niche | Nature (nature.com)
OHAUS Rotor, Angle, 24 × 1.5/2.0 ml, Sealable Model number R-A24 X 2/15MS:Centrifuges, | Fisher Scientific
OHAUS Rotor, Angle, 24 × 1.5/2.0 ml, Sealable Model number R-A24 X 2/15MS:Centrifuges, | Fisher Scientific (fishersci.com)
Direct identification of ALK and ROS1 fusions in non-small cell lung cancer from hematoxylin and eosin-stained slides using...
Direct identification of ALK and ROS1 fusions in non-small cell lung cancer from hematoxylin and eosin-stained slides using... (nature.com)
Advances in Translational Models to Study Fibrosis | The New York Academy of Sciences
Advances in Translational Models to Study Fibrosis | The New York Academy of Sciences (nyas.org)
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis | Nature
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis | Nature (nature.com)
Acute Flaccid Myelitis Task Force Update, May 2019 | Board of Scientific Counselors | CDC
Acute Flaccid Myelitis Task Force Update, May 2019 | Board of Scientific Counselors | CDC (cdc.gov)
Veterinary Molecular Diagnostics - Market Study by Global Industry Analysts, Inc.
Veterinary Molecular Diagnostics - Market Study by Global Industry Analysts, Inc. (strategyr.com)
Fall 2004 MCB Transcript | Molecular and Cell Biology
Fall 2004 MCB Transcript | Molecular and Cell Biology (mcb.berkeley.edu)
Master of Science Ecotoxicology
Master of Science Ecotoxicology (uni-koblenz-landau.de)
Chemistry Examples: Strong and Weak Electrolytes
Chemistry Examples: Strong and Weak Electrolytes (thoughtco.com)
Bacterial Resistance to Penicillin G by Decreased Affinity of Penicillin-Binding Proteins: A Mathematical Model - Volume 9,...
Bacterial Resistance to Penicillin G by Decreased Affinity of Penicillin-Binding Proteins: A Mathematical Model - Volume 9,... (wwwnc.cdc.gov)
Figure 2 - Bacterial Resistance to Penicillin G by Decreased Affinity of Penicillin-Binding Proteins: A Mathematical Model -...
Figure 2 - Bacterial Resistance to Penicillin G by Decreased Affinity of Penicillin-Binding Proteins: A Mathematical Model -... (wwwnc.cdc.gov)
DARPA Accelerated Molecular Discovery program - MIT EECS
DARPA Accelerated Molecular Discovery program - MIT EECS (eecs.mit.edu)
Leveraging the IPU for Molecular Dynamics Simulation
Leveraging the IPU for Molecular Dynamics Simulation (graphcore.ai)
Wolf References - Yellowstone National Park (U.S. National Park Service)
Wolf References - Yellowstone National Park (U.S. National Park Service) (nps.gov)
PuRe Publications | Max Planck Institute for Molecular Genetics
PuRe Publications | Max Planck Institute for Molecular Genetics (molgen.mpg.de)
Acute Flaccid Myelitis Task Force Update, December 2019 | Board of Scientific Counselors | CDC
Acute Flaccid Myelitis Task Force Update, December 2019 | Board of Scientific Counselors | CDC (cdc.gov)
Human skin color - Wikipedia
Human skin color - Wikipedia (en.wikipedia.org)
PDF] Physical chemistry of charged interfaces: Multiscale modelling and applications to Energy | Semantic Scholar
PDF] Physical chemistry of charged interfaces: Multiscale modelling and applications to Energy | Semantic Scholar (semanticscholar.org)
Prostate Cancer Workup: Approach Considerations, Prostate Cancer Screening, Prostate-Specific Antigen
Prostate Cancer Workup: Approach Considerations, Prostate Cancer Screening, Prostate-Specific Antigen (medscape.com)
Figure 1 - Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases...
Figure 1 - Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases... (wwwnc.cdc.gov)
Figure 2 - Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases...
Figure 2 - Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases... (wwwnc.cdc.gov)
Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases journal -...
Molecular Model of Prion Transmission to Humans - Volume 15, Number 12-December 2009 - Emerging Infectious Diseases journal -... (wwwnc.cdc.gov)
NEI Research News | National Eye Institute
NEI Research News | National Eye Institute (nei.nih.gov)
The Medical Model Doesn't Work for Mental Health
The Medical Model Doesn't Work for Mental Health (medscape.com)
NEI Research News | National Eye Institute
NEI Research News | National Eye Institute (nei.nih.gov)
Council Minutes -- May 2018 | National Institute on Aging
Council Minutes -- May 2018 | National Institute on Aging (nia.nih.gov)