Computer-based representation of physical systems and phenomena such as chemical processes.
A computer simulation developed to study the motion of molecules over a period of time.
Sequential operating programs and data which instruct the functioning of a digital computer.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
The properties, processes, and behavior of biological systems under the action of mechanical forces.
Organizations which provide an environment encouraging social interactions through group activities or individual relationships especially for the purpose of rehabilitating or supporting patients, individuals with common health problems, or the elderly. They include therapeutic social clubs.
An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
A mass spectrometry technique using two (MS/MS) or more mass analyzers. With two in tandem, the precursor ions are mass-selected by a first mass analyzer, and focused into a collision region where they are then fragmented into product ions which are then characterized by a second mass analyzer. A variety of techniques are used to separate the compounds, ionize them, and introduce them to the first mass analyzer. For example, for in GC-MS/MS, GAS CHROMATOGRAPHY-MASS SPECTROMETRY is involved in separating relatively small compounds by GAS CHROMATOGRAPHY prior to injecting them into an ionization chamber for the mass selection.
Non-invasive method of demonstrating internal anatomy based on the principle that atomic nuclei in a strong magnetic field absorb pulses of radiofrequency energy and emit them as radiowaves which can be reconstructed into computerized images. The concept includes proton spin tomographic techniques.
The guidelines and policy statements set forth by the editor(s) or editorial board of a publication.
A publication issued at stated, more or less regular, intervals.
"The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.
A quantitative measure of the frequency on average with which articles in a journal have been cited in a given period of time.
The scientific disciplines concerned with the embryology, anatomy, physiology, biochemistry, pharmacology, etc., of the nervous system.
The rate dynamics in chemical or physical systems.
Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The continuous sequential physiological and psychological maturing of an individual from birth up to but not including ADOLESCENCE.
Tests designed to assess neurological function associated with certain behaviors. They are used in diagnosing brain dysfunction or damage and central nervous system disorders or injury.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
A series of steps taken in order to conduct research.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)
The field of information science concerned with the analysis and dissemination of medical data through the application of computers to various aspects of health care and medicine.
Experimentally induced tumor that produces MELANIN in animals to provide a model for studying human MELANOMA.
Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.
Copies of a work or document distributed to the public by sale, rental, lease, or lending. (From ALA Glossary of Library and Information Science, 1983, p181)
The application of technology to the solution of medical problems.
Tumors or cancer of the SKIN.
The development and use of techniques to study physical phenomena and construct structures in the nanoscale size range or smaller.
An area of water mostly surrounded by land, usually smaller than a gulf, and affording access to the sea.
Single or multi-sheet notices made to attract attention to events, activities, causes, goods, or services. They are for display, usually in a public place and are chiefly pictorial.
Materials which have structured components with at least one dimension in the range of 1 to 100 nanometers. These include NANOCOMPOSITES; NANOPARTICLES; NANOTUBES; and NANOWIRES.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.

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)

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 ...
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 ...
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 ...
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 ...
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
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 ...
Check out our new paper and video on Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction. ...
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16.08.28 Theory and Applications of Computational Chemistry 2016, Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
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
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 ...
A foreword from Professor Kendall N. Houk for the Applied Computational Chemistry themed issue of Chemical Society Reviews. Applied Computational Chemistry
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 - ...
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 ...
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
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
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 ...
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 ...
Main Page of the Computational Chemistry Group. Scientific interests: Free Energy calculations, QM/MM method, PAW-method, Biological Nitrogen Fixation by Nitrogenase, sodium nitroprusside
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 ...
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 ...
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 ...
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 ...
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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.
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 ...
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.
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.
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
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)], ...
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 ...
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
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. ...
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 ...
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
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.. ...
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 ...
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 ...
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
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 ...
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. ...
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 ...
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 ...
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 ...
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
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 ...
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. ...
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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.
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 ...
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 ...
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 ...
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:. ...
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 ...
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 ...
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
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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
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
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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 ...
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 ...
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 ...
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 ...
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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
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
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.
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.
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.
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 ...
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.
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 ...
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
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 ...
Purchase Annual Reports in Computational Chemistry, Volume 7 - 1st Edition. Print Book & E-Book. ISBN 9780444538352, 9780444543028
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.. ...
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 ...
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 ...
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 ...
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
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 ...
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 ...
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.
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 ...
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 - ...
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.
Electrostatic interactions between ligands and their receptors are important factors for molecular recognition. Assessing the ligand-receptor electrostatic complementarity provide valuable information for molecular design. In this hands-on workshop we will focus on using Flare™, Cressets structure-based design application to design ligands that are electrostatically complementary to the protein active site. You will learn how to visualize ligand-protein interactions; design new molecules in the context of the active site; easily dock new molecule designs to a protein active site; and assess the electrostatic complementarity between ligands and protein.
Molecular modeling[edit]. Main article: Molecular modeling. Nonlinear optimization methods are widely used in conformational ... Gradient descent is used to update Weights in a Neural Network Model, i.e. update and tune the Model's parameters in a ... Also, agents are often modeled as being risk-averse, thereby preferring to avoid risk. Asset prices are also modeled using ... Space mapping is a concept for modeling and optimization of an engineering system to high-fidelity (fine) model accuracy ...
ISBN 978-0-471-33368-5. "Quantum Computational Software; Molecular Modeling; Visualization". www.q-chem.com. Retrieved 2020-01- ... "Advances in molecular quantum chemistry contained in the Q-Chem 4 program package". Molecular Physics. 113 (2): 184-215. doi: ... a molecular builder, and general visualization capabilities (MOs, densities, molecular vibrations, reaction pathways, etc.). ... by libwfa developed by Felix Plasser and co-workers Janus QM/MM interface YinYang Atom model without linked atoms ONIOM model ...
Korneev, K. V. (18 October 2019). "Mouse Models of Sepsis and Septic Shock". Molecular Biology. 53 (5): 704-717. doi:10.1134/ ... Immune cells not only recognise pathogen-associated molecular patterns but also damage-associated molecular patterns from ... The molecular character of this material was determined by Luderitz et al. in 1973. It was discovered in 1965 that a strain of ... The authors called for abandoning the use of mouse models in sepsis research; others rejected that but called for more caution ...
In QSAR modeling, the predictors consist of physico-chemical properties or theoretical molecular descriptors of chemicals; the ... Quantitative structure-activity relationship models (QSAR models) are regression or classification models used in the chemical ... Leach AR (2001). Molecular modelling: principles and applications. Englewood Cliffs, N.J: Prentice Hall. ISBN 978-0-582-38210-7 ... Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response ...
By studying animal models and keeping in mind the innate differences in CYP3A4 activation, investigators can better predict ... Gonzalez FJ (2007). "CYP3A4 and pregnane X receptor humanized mice". Journal of Biochemical and Molecular Toxicology. 21 (4): ... Robertson GR, Field J, Goodwin B, Bierach S, Tran M, Lehnert A, Liddle C (July 2003). "Transgenic mouse models of human CYP3A4 ... In addition to providing an in vivo model, humanized CYP3A4 mice (hCYP3A4) have been used to further emphasize gender ...
2011 "Multiscale Modeling" 2010 "Regulation & Control in Biological Systems" 2009 "Molecular Evolution" 2008 "Computational ... ". "Multiscale Modeling". "Regulation and Control in Biological Systems". "Molecular Evolution". "Computational Structural ... 2021 [BC]2 Basel Computational Biology Conference 2019 [BC]2 Basel Computational Biology Conference "Big Data in Molecular ... " "BC2 Conference". "[BC]2 "Big Data in Molecular Medicine"". "13th [BC]2 Conference 2017". "12th [BC]2 Conference 2015 - ...
2. Palms on an oceanic island". Molecular Ecology. 16 (14): 2910-2921. doi:10.1111/j.1365-294x.2007.03304.x. PMID 17614906. ... Gavrilets, Sergei; Vose, Arron (2007). "Case studies and mathematical models of ecological speciation. ... Wallis, G.P.; Trewick, Steve A. (2009). "New Zealand phylogeography: evolution on a small continent". Molecular Ecology. 18 (17 ...
... (DAAO; also OXDA, DAMOX) is an enzyme with the function on a molecular level to oxidize D-amino acids to ... Olney JW, Newcomer JW, Farber NB (November 1999). "NMDA receptor hypofunction model of schizophrenia". Journal of Psychiatric ... Pilone MS (November 2000). "D-Amino acid oxidase: new findings". Cellular and Molecular Life Sciences. 57 (12): 1732-47. doi: ... September 2008). "Antipsychotic drugs: comparison in animal models of efficacy, neurotransmitter regulation, and ...
Anon (2008). "A Special Issue in Honour of Professor Anthony J. Stone". Molecular Physics. 106 (12): 3. doi:10.1080/ ... Price, Sarah L. (1980). Model intermolecular pair potentials. ethos.bl.uk (PhD thesis). University of Cambridge. OCLC 557224619 ... Molecular Physics. 5 (5): 417-424. Bibcode:1962MolPh...5..417L. doi:10.1080/00268976200100471. ISSN 0026-8976. ...
"Quantum Computational Software; Molecular Modeling; Visualization". www.Q-Chem.com. Retrieved 2 January 2018. "Faculty Profile ... Molecular Physics, and Wires Computational Molecular Science. She has served as a guest editor for a special issue of J. Phys. ... Her Ph.D. research at the Fritz Haber Center focused on molecular dynamics in rare gas clusters and matrices. Upon completing ... In addition, she is an elected member of the International Academy of Quantum Molecular Science. In addition to her permanent ...
He later studied with Christopher A. Fields at New Mexico State University, gaining his PhD in molecular biology in 1992. From ... "Microbial gene identification using interpolated Markov models". Nucleic Acids Research. 26 (2): 544-8. doi:10.1093/nar/26.2. ... CS1 maint: discouraged parameter (link) "Recent Graduates , Molecular Biology". molb.research.nmsu.edu. Retrieved 15 September ...
Molecular Microbiology. 44 (6): 1575-87. doi:10.1046/j.1365-2958.2002.02978.x. PMID 12067345. SWISS-MODEL. Matched templates ... McDevitt CA, Hugenholtz P, Hanson GR, McEwan AG (June 2002). "Molecular analysis of dimethyl sulphide dehydrogenase from ... Model report Other data Dimethyl+sulfide:cytochrome+c2+reductase at the US National Library of Medicine Medical Subject ...
... and for the most typical models of relationships, Dk is close to 1, which means most of these models can be used to estimate ... Molecular Ecology. 9, 2056, 2015. ISSN 0962-1083 Legarra, Andres (2016). "Comparing estimates of genetic variance across ... However, different models may give different estimates of genetic variances. They found that expected genetic variances usually ... In this research, the researchers use the different relationship models to compare estimates of genetic variance components and ...
Locuson CW, Rock DA, Jones JP (June 2004). "Quantitative binding models for CYP2C9 based on benzbromarone analogues". ... Molecular Pharmacology. 68 (3): 644-51. doi:10.1124/mol.105.013763. PMC 1552103. PMID 15955872. ...
Troncale studied at the Catholic University of America from 1966 to 1970, and received his Ph.D. in 1970 in Molecular Biology. ... Systems Thinking and Dynamic Modeling Conference (June 25-27, 2000) Archived 2001-11-17 at archive.today. General info. ... Later in the 1970s he became Professor Cellular and Molecular Biology, and Director of the Institute for Advanced Systems ... Lenard Raphael Troncale (born 1943) is an American biologist, systems theorist, Professor Emeritus of Cellular and Molecular ...
Geyer MA, McIlwain KL, Paylor R (2002). "Mouse genetic models for prepulse inhibition: an early review". Molecular Psychiatry. ... Murine models are widely used to test hypotheses linking genetic components of various diseases with sensorimotor gating. While ... Dopamine, which plays a major role in schizophrenia, had been shown to regulate sensorimotor gating in rodent models. These ... Many animal studies of PPI are undertaken in order to understand and model the pathology of schizophrenia. Schizophrenia-like ...
Abbas A (2018). Cellular and molecular immunology. Elsevier. p. 447. ISBN 978-0-323-47978-3. Monroe EW, Daly AF, Shalhoub RF ( ... Andersen HH, Elberling J, Arendt-Nielsen L (September 2015). "Human surrogate models of histaminergic and non-histaminergic ... Haenisch B, Nöthen MM, Molderings GJ (November 2012). "Systemic mast cell activation disease: the role of molecular genetic ... Brady S (2012). Basic Neurochemistry - Principles of Molecular, Cellular and Medical Neurobiology. 225 Wyman Street, Waltham, ...
Molecular Ecology. 15 (2): 301. doi:10.1111/j.1365-294X.2006.02899.x. Dennis, C.; Wright, J. (2006). "Model Mentors". Nature. ... Butlin, R.; Rieseberg, L.; Smith., H. (2006). "Godfrey Hewitt - Recipient of 2005 Molecular Ecology Prize". Molecular Ecology. ... He was awarded the 2005 Molecular Ecology Prize, and he received a Lifetime Achievement Award for creative mentoring in science ... Butlin, R.; Rieseberg, L.; Smith., H. (2006). "Godfrey Hewitt - Recipient of 2005 Molecular Ecology Prize". ...
"Molecular modelling of the GABAA ion channel protein". Journal of Molecular Graphics & Modelling. 25 (5): 721-730. doi:10.1016/ ... Journal of Molecular Graphics and Modelling. 26 (4): 760-774. doi:10.1016/j.jmgm.2007.04.012. Miller PS, Aricescu AR (August ... Vijayan RS, Trivedi N, Roy SN, Bera I, Manoharan P, Payghan PV, Bhattacharyya D, Ghoshal N (November 2012). "Modeling the ... The ionotropic GABAA receptor protein complex is also the molecular target of the benzodiazepine class of tranquilizer drugs. ...
ISBN 978-0-9636769-4-8. Leach, Andrew R. (1996). Molecular Modelling. Harlow: Longman. pp. 83-85. ISBN 978-0-582-23933-3. ... Additionally, various important molecular properties calculated at MP3 and MP4 level are no better than their MP2 counterparts ... Helgaker, Trygve; Poul Jorgensen; Jeppe Olsen (2000). Molecular Electronic Structure Theory. Wiley. ISBN 978-0-471-96755-2. ... Pople, John A.; Binkley, J. Stephen; Seeger, Rolf (1976). "Theoretical models incorporating electron correlation". ...
Korneev, K. V. (18 October 2019). "Mouse Models of Sepsis and Septic Shock". Molecular Biology. 53 (5): 704-717. doi:10.1134/ ... Animal Testing Animal model BALB/c C57BL/6 Mouse models of colorectal and intestinal cancer Preclinical imaging Rat Park ... Information about mouse models from HOPES:Huntington's Disease Outreach Project for Education at Stanford Animal Model of ... They are widely considered to be the prime model of inherited human disease and share 99% of their genes with humans. With the ...
A tetrahedral model". Molecular Pharmacology. 28 (5): 391-9. PMID 2932631. Burt DR, Creese I, Snyder SH (April 1977). " ...
Kolafa, Jiří; Nezbeda, Ivo (May 1987). "Monte Carlo simulations on primitive models of water and methanol". Molecular Physics. ... Patchy particles are used as a shorthand for modelling anisotropic colloids, proteins and water and for designing approaches to ... Fusco, Diana; Charbonneau, Patrick (2013). "The crystallization of asymmetric patchy models for globular proteins in solution ... representation of the discontinous potential described above enables the simulation of patchy particles using molecular ...
In 2009, he joined Bar Ilan University as an associate professor at the Department of Chemistry leading the molecular modeling ... Molecular modelling, Computer-Aided Drug Design, and Chemoinformatics. Hanoch Senderowitz received his Ph.D. in 1993 from Tel ... "Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane ... Yosipof, Abraham; Senderowitz, Hanoch (2014). "Optimization of Molecular Representativeness". Journal of Chemical Information ...
Lamond AI, Spector DL (August 2003). "Nuclear speckles: a model for nuclear organelles". Review. Nature Reviews. Molecular Cell ... A second model proposes that proto-eukaryotic cells evolved from bacteria without an endosymbiotic stage. This model is based ... The first model known as the "syntrophic model" proposes that a symbiotic relationship between the archaea and bacteria created ... 2016). Molecular Cell Biology (Eighth ed.). New York: W.H. Freeman. ISBN 978-1-4641-8339-3. Alberts B, Johnson A, Lewis J, Raff ...
The first one is the one-ring embrace model, and the second one is the dimeric handcuff-model. The one-ring embrace model ... Haering CH, Löwe J, Hochwagen A, Nasmyth K (April 2002). "Molecular architecture of SMC proteins and the yeast cohesin complex ... Zhang N, Kuznetsov SG, Sharan SK, Li K, Rao PH, Pati D (December 2008). "A handcuff model for the cohesin complex". The Journal ... According to the handcuff model, each ring has one set of RAD21, SMC1, and SMC3 molecules. The handcuff is established when two ...
The Zucker rat was bred to be a genetic model for research on obesity and hypertension. They are named after Lois M. Zucker and ... August 1996). "Molecular cloning of rat leptin receptor isoform complementary DNAs--identification of a missense mutation in ... "Research Animal Models". CRiver.com. Charles River Laboratories. Archived from the original on 24 May 2013. Retrieved 5 August ... Like NOD mice, biobreeding rats are used as an animal model for Type 1 diabetes. The strain re-capitulates many of the features ...
It has a cage-like molecular structure, whose carbon skeleton can be viewed as three fused cyclohexane rings in the boat ... "Extensions in the use of plastic tetrahedral models". J. Chem. Educ. 42 (8): 408-412. doi:10.1021/ed042p408. CS1 maint: ... discouraged parameter (link) Hargittai, M.; Hargittai, I. (2013). "Polyhedral Molecular Geometries". In Senechal, M. (ed.). ...
If they are damaged, a molecular brake stops them from dividing until they are repaired. If they can't be repaired, they commit ... Cesare, Anthony J.; Reddel, Roger R. (2010). "Alternative lengthening of telomeres: Models, mechanisms and implications". ... Greenberg, RA (March 2005). "Telomeres, crisis and cancer". Current Molecular Medicine. 5 (2): 213-8. doi:10.2174/ ...
Liu, Dongyou (2017). Laboratory Models for Foodborne Infections. CRC Press. ISBN 9781498721684. Sails, Andrew (2014). Molecular ...
Single-neuron modeling[edit]. Main article: Biological neuron models. Even single neurons have complex biophysical ... We know from molecular biology that distinct parts of the nervous system release distinct chemical cues, from growth factors to ... Earlier models of memory are primarily based on the postulates of Hebbian learning. Biologically relevant models such as ... Lapicque introduced the integrate and fire model of the neuron in a seminal article published in 1907.[16] This model is still ...
Advances in the fields of molecular biology and genetics, as well as the use of animal models have been of great importance in ... "Human Molecular Genetics. 6 (10): 1647-56. doi:10.1093/hmg/6.10.1647. PMID 9300656.. ... Part A, Clinical and Molecular Teratology. 82 (2): 78-85. doi:10.1002/bdra.20426. PMID 18050313.. ... Mulliken JB, Gripp KW, Stolle CA, Steinberger D, Müller U (June 2004). "Molecular analysis of patients with synostotic frontal ...
Neuberger, M. S.; Honjo, T.; Alt, Frederick W. (2004). Molecular biology of B cells. Amsterdam: Elsevier. pp. 189-191. ISBN 0- ... B cells differentiate into plasma cells that produce antibody molecules closely modelled after the receptors of the precursor B ...
Sun T, Han X (2019). "Death versus dedifferentiation: The molecular bases of beta cell mass reduction in type 2 diabetes". ... "Projections of type 1 and type 2 diabetes burden in the U.S. population aged ,20 years through 2050: dynamic modeling of ... The Journal of Steroid Biochemistry and Molecular Biology. 114 (1-2): 40-3. doi:10.1016/j.jsbmb.2008.12.022. PMID 19444934.. ...
Molecular ageing in progeroid syndromes: Hutchinson-Gilford progeria syndrome as a model. Immun Ageing. 2009, 6: 4. PMC 2674425 ... Trends in molecular medicine. 2004, 9 (9): 370-5. PMID 13129702. doi:10.1016/S1471-4914(03)00162-X.. ...
"Journal of Molecular Biology. 354 (4): 789-800. doi:10.1016/j.jmb.2005.09.095. PMC 1403828. PMID 16277992.. ... 3D model (JSmol). *Interactive image. SMILES. *. CC(C)(C)NC(=O)[[email protected]@H]1CN(CCN1C[[email protected]](C[[email protected]@H](Cc2ccccc2)C(=O)N[[email protected]]3c4ccccc4C[[email protected] ...
... and an incorrect model of the anatomy and physiology of internal organs.[8][59][60][61][62][63] ... Trends in Molecular Medicine. 20 (9): 473-76. doi:10.1016/j.molmed.2014.06.007. PMID 25150944.. ... molecular biology, biophysics, and other natural sciences to clinical practice, using scientific methods to establish the ... Snyderman and Weil remarked that by the early twentieth century the Flexner model had helped to create the 20th-century ...
Due to scanty fossil evidence it is unclear which ape or apes contributed to the modern hominid clade, but molecular evidence ... and thus modern cycads are not a good model for a "living fossil".[17] ...
One possible way to achieve this, which has been successful in mouse models, is to use inhibitors of Ras activation in order to ... Nature Reviews Molecular Cell Biology. 10 (4): 276-86. doi:10.1038/nrm2654. PMID 19305417. MacDonald BT, Tamai K, He X (July ...
... which is a central premise of his model of selection in nature.[5] Later in his career, Castle would refine his model for ... Methods in Molecular Biology, Springer US, pp. 15-25, doi:10.1007/978-1-4939-9865-4_3, ISBN 9781493998654. , PMID 31541435. ... are based on a comparison of single QTL models with a model assuming no QTL. For instance in the "interval mapping" method[23] ... Methods in Molecular Biology, Springer US, 2072, pp. 15-25, doi:10.1007/978-1-4939-9865-4_3, ISBN 9781493998654. , PMID ...
Molecular properties can be modeled through sedimentation velocity analysis or sedimentation equilibrium analysis. During the ... it had exactly the same molecular weight.[11][12] How something of such a large molecular mass could be consistently found, ... Cao, W., Demeler B. Modeling Analytical Ultracentrifugation Experiments with an Adaptive Space-Time Finite Element Solution for ... Sedimentation Velocity Analysis of Heterogeneous Protein-Protein Interactions: Lamm Equation Modeling and Sedimentation ...
Resulting information can be used to build biological models, design experiments, or get up to speed in an area of research. ... The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems ... "Best of Show Award Winners Named at the Fifteenth International Molecular Medicine Tri-Conference" (Press release). Cambridge ... "Ingenuity Systems releases IPA™ 5.0 software, offering new biomarker and molecular toxicology capabilities" (PDF) (Press ...
1999). "Synthesis of multi-subunit domain gonadotropin complexes: a model for alpha/beta heterodimer formation". Biochemistry. ... Molecular function. • follicle-stimulating hormone activity. • ربط بروتيني. • فعالية الهرمون. Cellular component. • ...
Brioche T, Pagano AF, Py G, Chopard A (April 2016). "Muscle wasting and aging: Experimental models, fatty infiltrations, and ... cellular and molecular responses to depressed metabolism and low temperature". Physiol. Rev. 83 (4): 1153-81. doi:10.1152/ ... Brioche T, Pagano AF, Py G, Chopard A (April 2016). "Muscle wasting and aging: Experimental models, fatty infiltrations, and ...
... with terms containing particulate volumes and refractive indices replaced with terms for molecular polarizability.[8] ... Rayleigh sky model. *Ricean fading. *Optical phenomenon. *Dynamic light scattering. *Raman scattering ... can also be written in terms of individual molecules by expressing the dependence on refractive index in terms of the molecular ...
Função molecular. •extracellular matrix structural constituent. •protein binding. •extracellular matrix constituent conferring ... 2009). «Integrative predictive model of coronary artery calcification in atherosclerosis». Circulation. 120 (24): 2448-54. PMC ... Dyksterhuis LB, Weiss AS (2010). «Homology models for domains 21-23 of human tropoelastin shed light on lysine crosslinking». ... use of recombinantly expressed human elastin polypeptides as a model for investigations of structure and self-assembly of ...
... since more sophisticated models of the scanner Physics can be incorporated into the likelihood model than those used by ... 2003). "11C-metomidate PET imaging of adrenocortical cancer". European Journal of Nuclear Medicine and Molecular Imaging. 30 (3 ... Crump Institute for Molecular Imaging. Archived from the original (PDF) on May 18, 2015.. ... Vardi, Y.; L. A. Shepp; L. Kaufman (1985). "A statistical model for positron emission tomography". Journal of the American ...
Volkow ND, Koob GF, McLellan AT (January 2016). "Neurobiologic Advances from the Brain Disease Model of Addiction". N. Engl. J ... Molecular Neuropharmacology: A Foundation for Clinical Neuroscience (2nd ed.). New York: McGraw-Hill Medical. pp. 364-375. ISBN ... Thus, kindling has been suggested as a model for temporal lobe epilepsy in humans, where stimulation of a repetitive type ( ... Morimoto K, Fahnestock M, Racine RJ (2004). "Kindling and status epilepticus models of epilepsy: Rewiring the brain". Prog ...
Feugier, François (14 December 2006). Models of Vascular Pattern Formation in Leaves (PhD Thesis). University of Paris VI.. ... On the basis of molecular genetics, Eckardt and Baum (2010) concluded that "it is now generally accepted that compound leaves ... Read and Stokes (2006) consider two basic models, the "hydrostatic" and "I-beam leaf" form (see Fig 1).[40] Hydrostatic leaves ... "Modeling and Visualization of Leaf Venation Patterns". ACM SIGGRAPH 2005 Papers. 24 (3): 702-711. CiteSeerX 10.1.1.102.1926. ...
Disease models. Animal models and in particular non-human primates are being used to study different aspects of Ebola virus ... Klenk, Hans-Dieter; Feldmann, Heinz (2004). Ebola and Marburg viruses: molecular and cellular biology (Limited preview). ... Developments in organ-on-a-chip technology have led to a chip-based model for Ebola haemorrhagic syndrome.[262] ... Trends in Molecular Medicine. 12 (5): 206-15. doi:10.1016/j.molmed.2006.03.006. PMID 16616875.. ...
"Interaction model - Probing space weather with comets". KVI atomics physics. Archived from the original on 2006-02-13. ... "Rosetta finds molecular oxygen on comet 67P (Update)". phys.org. Retrieved 2017-01-08.. ...
Main articles: Mandala (political model), Greater India, and Indosphere. The Rajamandala (or Raja-mandala; circle of states) ... Hasegawa, Masami (2017). "Phylogeny mandalas for illustrating the Tree of Life". Molecular Phylogenetics and Evolution. 117: ... This mandala is generally structured according to the model of the universe as taught in a Buddhist classic text the Abhidharma ... but it originally meant to represent wholeness and a model for the organizational structure of life itself, a cosmic diagram ...
Molecular structureEdit. The 154 kb chloroplast DNA map of a model flowering plant (Arabidopsis thaliana: Brassicaceae) showing ... Alternative model of replicationEdit. One of the main competing models for cpDNA asserts that most cpDNA is linear and ... Leading model of cpDNA replicationEdit. Chloroplast DNA replication via multiple D loop mechanisms. Adapted from Krishnan NM, ... Alberts B (2002). Molecular biology of the cell (4. ed.). New York [u.a.]: Garland. ISBN 978-0-8153-4072-0. .. ...
"WHO Model List of Essential Medicines (19th List)" (PDF). World Health Organization. April 2015. Archived (PDF) from the ... Seyfizadeh, Narges; Seyfizadeh, Nayer; Hasenkamp, J; Huerta-Yepez, S (2016). "A molecular perspective on rituximab: A ...
"Molecular Reproduction, Development and Genetics at IISc". www.mrdg.iisc.ernet.in.. ... "A Small Animal Model of ETEC-Mediated Diarrhea - Grand Challenges". gcgh.grandchallenges.org.. ... She is currently the Chairperson of the Department of Molecular Reproduction, Development and Genetics[1] and the Co-chair of ... In 1993, she was appointed as Assistant Professor at the Department of Molecular Reproduction, Development and Genetics,[12] ...
Ertl P.; Rohde B.; Selzer P. (2000). „Fast calculation of molecular polar surface area as a sum of fragment based contributions ...
They have combined molecular and genetic approaches to answer some of Darwins key questions about the natural variation of ... developing models for the evolution of genetic systems, including sex and recombination, inbreeding and outbreeding, separate ... Distinguished for his work on molecular evolution, in particular on the role of stochastic events in determining the rate of ...
Ertl P.; Rohde B.; Selzer P. (2000). „Fast calculation of molecular polar surface area as a sum of fragment based contributions ...
"Molecular Biology of the Cell. 6 (5): 509-24. doi:10.1091/mbc.6.5.509. PMC 301212 . PMID 7545030.. ... American Journal of Respiratory Cell and Molecular Biology. 24 (2): 101-7. doi:10.1165/ajrcmb.24.2.4264. PMID 11159042.. ... Spacefilling model of substance P. Identifiers. Symbol. TAC1. Alt. symbols. TAC2, NKNA. ...
Russo J, Russo I (1987). "Biological and molecular bases of mammary carcinogenesis". Laboratory Investigation 57 (2): 112-37. ... but the parallelism between the DMBA-induced rat mammary carcinoma model and the human situation is striking. …Abortion would ...
Quantum chemistry calculations[2][3][4][5][6][7] and molecular mechanics simulations[8][9][10] (molecular modeling in terms of ... GPU accelerated molecular modelling software[edit]. Programs[edit]. *Abalone - Molecular Dynamics (Benchmark) ... Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.[1] ... 2008). "GPU acceleration of cutoff pair potentials for molecular modeling applications". In CF08: Proceedings of the 2008 ...
The first part of the tutorial will provide a quick review of basic molecular simulation techniques. Please note that most ... Some experience with molecular simulations and knowledge of statistical mechanics are required to take full advantage of the ... performing and analyzing simulations with empirical potentials using the LAMMPS molecular dynamics software, and showcase ...
J Chem Inf Model. 2009 Nov;49(11):2512-27. doi: 10.1021/ci9003706. Comparative Study; Research Support, N.I.H., Extramural; ... Molecular docking screens using comparative models of proteins.. Fan H1, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. ... We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic ... Even for single models, the models are significantly more enriching than the template structure if the template is paralogous ...
Looks like you are currently in United States but have requested a page in the Comoros site. Would you like to change to the Comoros site?. ...
... Services. The Computational Chemistry and Molecular Modeling ... Computational Chemistry and Molecular Modeling Support Group * Shared and Core Facilities * Computational Chemistry and ... Quantum mechanical (QM) or molecular mechanical (MM) calculations to evaluate the importance of residues in and around active ... the group is able to develop structures that mimic the behavior of molecules or molecular reactions. Background. Types of ...
Molecular Modeling of Chemoreceptor:Ligand Interactions. In: Manson M. (eds) Bacterial Chemosensing. Methods in Molecular ... MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD et al (1998) All-atom empirical potential for molecular modeling ... Vainio MJ, Puranen JS, Johnson MS (2009) ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model ... Similar computational strategies can be used for the molecular modeling of a series of ligand:protein receptor interactions. ...
... ... The Computational Chemistry and Molecular Modeling Support Group helps intramural researchers create structural models of ... Quantum mechanical (QM) or molecular mechanical (MM) calculations to evaluate the importance of residues in and around active ... the group is able to develop structures that mimic the behavior of molecules or molecular reactions. ...
JNeurosci Online ISSN: 1529-2401. The ideas and opinions expressed in JNeurosci do not necessarily reflect those of SfN or the JNeurosci Editorial Board. Publication of an advertisement or other product mention in JNeurosci should not be construed as an endorsement of the manufacturers claims. SfN does not assume any responsibility for any injury and/or damage to persons or property arising from or related to any use of any material contained in JNeurosci.. ...
Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non- ... Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non- ... Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, ... Biomolecule simulation Computational methods Membrane proteins Molecular modeling Protein structure prediction Simulation ...
MolyMod molecular models sets are for use by students, teachers, and researchers. The popular Prentice Hall sets for general ... and organic chemistry utilize Molymod atoms and bond links and may be upgraded or customized with additional model parts. ... Molecular Model Sets ::.. Top quality Molymod molecular model sets are for use by students, teachers, and researchers. The ... Build custom model sets or upgrade your current sets with Molymod components.. Click on the catalog number links for ordering ...
Students can construct models of water, carbon dioxide, hydrogen chloride, and more. Includes a teacher manual and student ... Orbit Molecular Models Kit. Item # 840222 *bvseo_sdk, java_sdk, bvseo-4.0.0 ... This package contains 12 model sets in one. Students can construct models of water, carbon dioxide, hydrogen chloride, and more ... This package contains 12 model sets in one. Students can construct models of water, carbon dioxide, hydrogen chloride, and more ...
Final model of the chromatosome particle based on the position of H1d_C as shown in Figure B. In this model, H1d_C is seen to ... Molecular modeling of the chromatosome particle.. Bharath MM1, Chandra NR, Rao MR. ... The two models differ from each other only in their first 26 residues (shown in red). The first figure shows the model where ... its structure and location in the nucleosome has been studied by molecular modeling methods. The structure of the globular ...
Molecular Modelling & Engineering Group. Molecular Modelling & Engineering Group We are a research group working at the ... Our research is focused on the application of molecular simulation methods to tackle problems in the fields of chemical and ... By developing and applying molecular simulation techniques to efficiently investigate these processes we aim at addressing open ...
The enormous development of computer hard drive space means that the molecular modeling field is developing very quickly. ... Andrew R. Leach: Molecular Modelling, Principles and Applications, 2ed, samt utdelat material. ... goal with this course is to provide an overview of the methods and techniques which are used within modern molecular modeling. ... A total of 20 university credits (hp) in Biotechnology or Molecular Biology. 20 university credits (hp) of Chemistry, possibly ...
Molecular modeling and simulation by Tamar Schlick; 1 edition; First published in 2010; Subjects: Models, Computer simulation, ... Molecular modeling and simulation an interdisciplinary guide 2nd ed. Tamar Schlick Published 2010 by Springer in New York . ... Are you sure you want to remove Molecular modeling and simulation from your list? ... Citation ,publisher = Springer ,ol = 25101280M ,publication-place = New York ,title = Molecular modeling and simulation ,url = ...
Aim: To introduce students to molecular modelling techniques as applied to biological systems with particular emphasis on the ... Classical Methods: Molecular Mechanics, Molecular Dynamics & Metropolis Monte Carlo; thermodynamic and transport properties; ... application of computer modelling to molecular aggregates such as membranes. Illustrative Bibliography: *G.H. Grant & W.G. ... Syllabus: Coordinate systems: how to describe 3-D molecular structure. Potential energy surfaces: quantum & empirical; ...
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 ...
Structural modeling of complexes of biomedical interest. We generate molecular models to understand how proteins interact to ... 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. ...
Molecular design software Molecular graphics Molecular modelling Ribbon diagram Software for molecular mechanics modeling Space ... A molecular model, is a physical model that represents molecules and their processes. The creation of mathematical models of ... Contains a mixture of physical models and molecular graphics. Free to use images of molecular models made by Miramodus ltd. ... Molecular graphics has replaced some functions of physical molecular models, but physical kits continue to be very popular and ...
... 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) ...
... a model of the potential energy of a molecular system. The result is a model that is accurate, transferable, and billions of ... However, these models face a tradeoff between computational cost and accuracy. The alternative approach to molecular dynamics-i ... Scientists have now used a machine learning technique called transfer learning to create a novel model of molecular motion. The ... New deep learning models predict the interactions between atoms in organic molecules. These models could help computational ...
MODELLER - comparative protein structure modeling by satisfaction of spatial restraints * Oslet - a molecular modeling and ... Amber - ($) "Assisted Model Building with Energy Refinement" is a set of molecular mechanical force fields for the simulation ... Ghemical - a molecular modelling package; graphical user interface is built on GTK2; both quantum-mechanical and forcefield- ... AMMP - a modern full-featured molecular mechanics, dynamics and modeling program * AutoDock - a suite of automated docking ...
The molecular disease model for melanoma is the first of many such models planned by Cancer Commons, the open science ... announces the publication of a molecular disease model of melanoma (MDMM) which classifies the disease into molecular subtypes ... The paper, titled "Molecular Disease Model for Melanoma," by Vidwans et al, was published in the March 30th issue of PLoS ONE. ... A molecular subtype of melanoma is loosely defined as those tumors containing the same set of molecular (primarily genetic) ...
The Challenge of Classifying Metastatic Cell Properties by Molecular Profiling Exemplified with Cutaneous Melanoma Cells and ... Molecular & Cellular Proteomics March 1, 2020, First published on December 31, 2019, 19 (3) 478-489; https://doi.org/10.1074/ ...
... ... PathAI developed a machine learning (ML) model-based pipeline to predict tumor molecular phenotypes from hematoxylin and eosin ... ML models were trained using over 1.6 million annotations of cancer cell and tissue histological features provided by board ... Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes. ...
BB2285 Project in Molecular Modelling 5.0 credits Projekt i molekylär modellering Course Syllabus. Established Course Syllabus ... This course is an extension of the course Molecular Modeling BB2280, and the aim is that the student should use the theoretical ... The project should involve using at least two different modern molecular modeling software packages. Finally the project will ... The student must have started or completed the course Molecular Modeling BB2280. The prerequisites for this course are ...
... B.G. Sumpter*, R.E. Tuzun, D.W. Noid, K. Solhberg. Oak ... Computer simulation and modeling have become powerful tools for understanding the structure and properties of a broad range of ... Fifth Foresight Conference on Molecular Nanotechnology.. There will be a link from here to the full article when it is ... and property prediction/modeling. A number of provocative results demonstrating the unique behavior of matter at the nanometer ...
Learn more about the Protein Biochemistry & Molecular Modeling Group and its key staff. ... Protein Biochemistry & Molecular Modeling Group key staff. Key staff table Name. Title. Email. Phone. ... Y. V. Sergeev, R. C. Caruso, M. R. Meltzer, N. Smaoui, I. M. MacDonald and P. A. Sieving: Molecular modeling of retinoschisin ... Molecular modeling indicates distinct classes of missense variants with mild and severe XLRS phenotypes. Hum Mol Genet, 22(23 ...
The jellium model is effective to explain subglobular clusters such as icosahedral clusters. To broaden the scope of this model ... Prediction of stable clusters based on the jellium model is limited because of the usual assumption of their spherical symmetry ... Here the authors propose a symmetry adapted orbital model by quantum chemistry calculations for the prediction of stable ... Many stable substances such as clusters have been predicted based on the jellium model, which usually assumes that their ...
... Dave Kristofferson kristoff at NET.BIO.NET Fri Apr 22 19:19:21 EST 1994 *Previous ...
  • Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. (wikipedia.org)
  • mdcore - an open-source platform-independent library for molecular dynamics simulations on modern shared-memory parallel architectures. (wikipedia.org)
  • 1) The use of multiple short molecular dynamics (MD) docking simulations, with residues within the binding pocket of the receptor unconstrained, so that the binding modes of the ligand in the binding pocket may be exhaustively examined. (springer.com)
  • Abalone - a GPU accelerated program for molecular dynamics simulations of proteins, DNA, ligands. (bioinformatics.org)
  • Perform intermediate level quantum mechanical and molecular mechanical simulations. (kth.se)
  • Molecular simulations methods can provide complementary information to experimental studies in the ongoing effort to accurately characterize the structural properties of DNCs and understand the impact that these features have on the thermodynamic and dynamic behavior of confined guest phases. (aiche.org)
  • Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo. (wikipedia.org)
  • The more advanced, computer-based molecular models of DNA involve molecular dynamics simulations and quantum mechanics computations of vibro-rotations, delocalized molecular orbitals (MOs), electric dipole moments, hydrogen-bonding, and so on. (wikipedia.org)
  • Computer molecular modeling allows both animations and molecular dynamics simulations that are very important to understand how DNA functions in vivo. (wikipedia.org)
  • Molecular Modeling Techniques in Materials Science explores the impact of using molecular modeling for various simulations in industrial settings. (routledge.com)
  • Quanta will automatically append as a suffix a .msf to the file name, where msf stands for molecular simulations file. (csbsju.edu)
  • A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. (mdpi.com)
  • Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. (mdpi.com)
  • Atomistic simulations have the potential to elucidate the molecular basis of biological processes such as protein misfolding in Alzheimer's disease or the conformational changes that drive transcription or translation. (bcr.org)
  • These groups of conformations become the states of our model and we can simply count transitions between states in our simulations to determine the probabilities of going from one to another. (bcr.org)
  • MSMs also provide a means of aggregating the data from many simulations into a single model. (bcr.org)
  • Moreover, just as it is possible to build up a road map by assembling information representing different locations, a larger, more comprehensive molecular kinetics map can be assembled from many shorter simulations. (bcr.org)
  • The Institute is now able to gather detailed molecular information and simulations to identify chemical mechanisms occurring in industrial processes. (edu.au)
  • Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. (osti.gov)
  • Fine-tuning of the parametrization of molecular dynamics simulations. (irbbarcelona.org)
  • We analyse protein flexibility using massive molecular dynamics simulations. (irbbarcelona.org)
  • 6. I can make this research more concrete for my students by showing them images and videos of the molecules I studied, and leading them in basic molecular simulations of their own. (scienceteacherprogram.org)
  • 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. (nih.gov)
  • New deep learning models predict the interactions between atoms in organic molecules. (energy.gov)
  • Molecular dynamics is the study of how atoms and molecules move and interact based on traditional Newtonian physics. (energy.gov)
  • This is the fastest and most accurate model of small organic molecules to date. (energy.gov)
  • In nanoscience , it could advance modeling of how tiny structures grow and how molecules are arranged in self-assembled soft materials. (energy.gov)
  • The result is the best-to-date empirical model of small organic molecules, in terms of both speed and accuracy. (energy.gov)
  • Is the structure of MHCII known with the coordinates so that this input can be used to model and study the interaction between the molecules?Can somebody throw some light on this? (bio.net)
  • In this poster we present an overview of a number of novel computational techniques that can be used to examine the structure and properties of materials (ranging from small molecules to polymers) and demonstrate their application to molecular nanotechnology: dynamics of nano-structured materials, nano- fluidics, nano-tribology, control dynamics of nano-sized objects, and property prediction/modeling. (foresight.org)
  • Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. (wikipedia.org)
  • Whereas molecular models of DNA molecules such as closely packed spheres (CPK models) made of plastic or metal wires for skeletal models are useful representations of static DNA structures, their usefulness is very limited for representing complex DNA dynamics. (wikipedia.org)
  • Although DNA consists of relatively rigid, very large elongated biopolymer molecules called fibers or chains (that are made of repeating nucleotide units of four basic types, attached to deoxyribose and phosphate groups), its molecular structure in vivo undergoes dynamic configuration changes that involve dynamically attached water molecules and ions. (wikipedia.org)
  • Such varying molecular geometries can also be computed, at least in principle, by employing ab initio quantum chemistry methods that can attain high accuracy for small molecules, although claims that acceptable accuracy can be also achieved for polynuclelotides, and DNA conformations, were recently made on the basis of vibrational circular dichroism (VCD) spectral data. (wikipedia.org)
  • Molecular Modeling in Drug Design" Molecules 24, no. 2: 321. (mdpi.com)
  • Introduce chemical formulas of common compounds, model how to build molecules, explain how to complete the worksheet, and have LEGOS available to students for to investigate independently. (buzzine.com)
  • Study the structure and chemical composition of DNA, RNA and biochemical molecules with these high-quality molecular models. (buzzine.com)
  • Objective 1) Using a model building kit, construct models of a variety of simple covalent molecules. (buzzine.com)
  • A molecular model, is a physical model that represents molecules and their processes. (wikipedia.org)
  • Hello, In the Kinetic-Molecular model for gas molecules in a container it is assumed that the square of the x-y-z velocity components is the same, how is it possible that we assume this? (physicsforums.com)
  • and in particular, we're working to sort out what makes the electrons move from molecule A to molecule B." Scientists like Newton are developing models to understand these interactions in molecular systems, where complex molecules communicate electronically across long distances. (bnl.gov)
  • Matt has experience in both Molecular Mechanics and Quantum Chemistry calculations, allowing for the detailed study of single molecules through to systems of millions of atoms in size. (edu.au)
  • We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. (osti.gov)
  • Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. (osti.gov)
  • Use these colorful, sturdy, wooden models to help students visualize a number of molecules. (flinnsci.com)
  • Use these colorful, sturdy, wooden models to help your students visualize molecules, such as C 4 H 10 , C 4 H 8 , BeH 2 , CCl 4 , XeF 4 , PF 3 Cl 2 and SF 6 . (flinnsci.com)
  • We investigate the impact of choosing regressors and molecular representations for the construction of fast machine learning (ML) models of thirteen electronic ground-state properties of organic molecules. (google.com)
  • The models at lower left and right show the molecules' backbone. (sciencephoto.com)
  • Create Customized Models and Molecules. (wardsci.com)
  • Why: To foster student appreciation for-and understanding of-the way scientists use computers to model molecules. (scienceteacherprogram.org)
  • The modeling covered in this book ranges from methods for small chemical to large biological molecules and materials. (eurobuch.com)
  • Build custom organic or bio-molecules models or choose the best student set for your needs. (indigo.com)
  • 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 isn't available. (nih.gov)
  • Increasingly useful in materials research and development, molecular modeling is a method that combines computational chemistry techniques with graphics visualization for simulating and predicting the structure, chemical processes, and properties of materials. (routledge.com)
  • The scope of the journal includes all aspects of molecular modeling and computational chemistry , including. (elsevier.com)
  • With its comprehensive coverage of important research fields in molecular and materials science, this is a must-have for all organic, inorganic and biochemists as well as materials scientists interested in applied theoretical and computational chemistry. (eurobuch.com)
  • Molecular Modeling of Geochemical Reactions: An Introduction applies computational chemistry to geochemical problems. (researchandmarkets.com)
  • Molecular docking screens using comparative models of proteins. (nih.gov)
  • Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. (springer.com)
  • Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical, and biosciences interested in utilizing this powerful technology. (springer.com)
  • The inset shows a superposition of different HMG-box proteins that were used as templates to model the H1d_C. ( B and C ) Two alternate models proposed for the whole H1d_C. The two models differ from each other only in their first 26 residues (shown in red). (nih.gov)
  • We generate molecular models to understand how proteins interact to form specific complexes that are fundamental in biological processes. (bsc.es)
  • Such chemical dynamics and biochemical reactions of DNA are much more complex than the molecular dynamics of DNA physical interactions with water, ions and proteins/enzymes in living cells. (wikipedia.org)
  • Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models. (povray.org)
  • To predict whether either of the CYP6Z1 and CYP6Z2 proteins might potentially metabolize DDT, we generated and compared molecular models of these two proteins with and without DDT docked in their catalytic sites. (pnas.org)
  • Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions, and notes on troubleshooting and avoiding common pitfalls. (springer.com)
  • The 150 credits should include a minimum of 20 credits within the fields of Mathematics, Numerical Analysis and Computer Sciences, 5 of these must be within the fields of Numerical Analysis and Computer Sciences, 20 credits of Chemistry, possibly including courses in Chemical Measuring Techniques and 20 credits of Biotechnology or Molecular Biology. (kth.se)
  • A total of 20 university credits (hp) in Biotechnology or Molecular Biology. (kth.se)
  • This model can capture a diversity of chemical processes, and it is broadly applicable to fields such as materials science, biology, and chemistry. (energy.gov)
  • Cancer Commons puts the patient at the front end of a remarkable experiment in 'translational medicine' - one in which basic molecular biology, computational methods and a network of experts and institutions collaborate to work out personalized medical solutions," said Donald Kennedy, Ph.D., Editor-in-Chief, Science (2000-2008). (medindia.net)
  • Today's popular depression models creatively merge ethologically valid behavioral assays with the latest technological advances in molecular biology and automated video-tracking. (nih.gov)
  • The discovery of numerous non-coding RNAs has dramatically changed our understanding of cell biology, especially the pathophysiology of breast cancer and we aim to investigate their role in breast cancer development using 3D models. (ntu.ac.uk)
  • The Ahmed and Coutts groups are within the world-leading REF2014 Biomedical Sciences Research Centre and has experience of a range of molecular cell biology techniques, including mammalian cell culture, 3D cultures, expression analysis, immunofluorescence, real time QPCR and Western blot analysis. (ntu.ac.uk)
  • Applicants should hold, or be expected to hold, an UK Master's degree (or UK equivalent according to NARIC) with a minimum of a commendation, and/or a UK 1stClass / 2.1 Bachelor's Honour's Degree (or UK equivalent according to NARIC) in Cell Biology, Biochemistry, Molecular Biology, or a related Biosciences related subject. (ntu.ac.uk)
  • To see more employment opportunities with European Molecular Biology Laboratory (EMBL), please click here . (jobs.ac.uk)
  • This workshop intends to gather theoretical physicists specialized in statistical physics and soft matter, and working on different subjects related to molecular and cell biology, but using very similar paradigms and tools. (cecam.org)
  • The popular Prentice Hall sets for general and organic chemistry utilize Molymod atoms and bond links and may be upgraded or customized with additional model parts. (sigmaaldrich.com)
  • The method is central to many questions in modern chemistry, and computer models are a powerful tool for answering these questions. (energy.gov)
  • GAMESS - the "General Atomic and Molecular Electronic Structure System" is a general ab initio quantum chemistry package. (bioinformatics.org)
  • Molecular models are as vital a tool for the study of chemistry as calculators are for the study of mathematics. (buzzine.com)
  • 23/12/2015 In this Article: Paper Tetrahedrons 2D Planar Models 3D Models Community Q&A. You may be studying organic chemistry, or just do it for fun. (buzzine.com)
  • JMGM is published in association with two of the largest and most active professional societies in the field: the Molecular Graphics and Modelling Society (MGMS) and the Computers in Chemistry (COMP) Division of the American Chemical Society . (elsevier.com)
  • NIH Guide to Molecular Modeling b. docking tutorial c. organic chemistry resources d. molecular modeling e. molecular graphics f. (csbsju.edu)
  • Physical models of atomistic systems have played an important role in understanding chemistry and generating and testing hypotheses. (wikipedia.org)
  • The course is designed to give students in chemistry and related subjects an introduction to the theory for molecular modeling, and use of modeling as a tool in chemical research. (uio.no)
  • Chemistry has long been taught using physical models, but ours are scaled precisely from accurrate experimental and quantum chemical geometries. (shapeways.com)
  • Yang, Qian, Sing-Long, Carlos A., and Reed, Evan J.. Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics . (osti.gov)
  • It showcases new developments and applications of computational quantum chemistry, statistical mechanics, molecular simulation and theory, and continuum and engineering process simulation. (springer.com)
  • In this new research, researchers first trained a neural network on a large set of density functional theory data, one the most popular quantum mechanics methods for studying molecular systems. (energy.gov)
  • We discuss recent advances in molecular simulation methods designed to model these complex materials, with particular emphasis placed on the those that are based in statistical mechanics (e.g. (aiche.org)
  • They have recently removed one of the best narrative descriptions of molecular mechanics and dynamics I have found, but I hope they restore it soon. (csbsju.edu)
  • The MacroModel program suite from Schr dinger, Inc. allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution. (povray.org)
  • Explain strengths and weaknesses of different models (molecular mechanics, semi-empirical, wavefunction based and density functional theory). (uio.no)
  • We use molecular dynamics and statistical mechanics to examine anomalous forms of nucleic acids. (irbbarcelona.org)
  • We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic structures and comparative models with known ligands. (nih.gov)
  • For the majority of the targets, the consensus enrichment for multiple models was better than or comparable to that of the holo and apo X-ray structures. (nih.gov)
  • c) Distribution of N-DOPE statistical potential score for comparative models (black and red bars for models based on holo and apo templates, respectively) and target X-ray structures (empty blue bars). (nih.gov)
  • Many stable substances such as clusters have been predicted based on the jellium model, which usually assumes that their structures are approximately spherical. (nature.com)
  • Although such initial studies of DNA structures with the help of molecular models were essentially static, their consequences for explaining the in vivo functions of DNA were significant in the areas of protein biosynthesis and the quasi-universality of the genetic code. (wikipedia.org)
  • Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists. (wikipedia.org)
  • 2) Draw Lewis structures and/or structural formulas of selected models. (buzzine.com)
  • After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
  • A kit that can be used for demonstrating not only organic structures, but also inorganic structures and molecular geometry. (flinnsci.com)
  • Molecular structures and properties at hybrid density functional theory (DFT) level of theory used for training and testing come from the QM9 database [Ramakrishnan et al, Scientific Data 1 140022 (2014)] and include dipole moment, polarizability, HOMO/LUMO energies and gap, electronic spatial extent, zero point vibrational energy, enthalpies and free energies of atomization, heat capacity and the highest fundamental vibrational frequency. (google.com)
  • The SSCM strategy is built upon a hypothesis, that is, similar compounds are most probably predicted more accurately by a same submodel among a model population, which can be concluded from the fact that models employing a different set of descriptors can predict compounds with specific structures more accurately. (wiley.com)
  • ED: Buch], [PU: Wiley VCH Verlag GmbH], Neuware - Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. (eurobuch.com)
  • EAN: 9783527330218], Neubuch, [SC: 0.0], [PU: Wiley VCH Verlag Gmbh Sep 2011], MATERIALWISSENSCHAFT, Neuware - Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. (eurobuch.com)
  • You can create molecular structures the whole class can see. (sargentwelch.com)
  • d) Distribution of root-mean-square deviation of the non-hydrogen atoms in binding site residues (RMSD bs ) between a comparative model and a target X-ray structure. (nih.gov)
  • The reason for the difference between graphite and diamond lies in their molecular structure--how the carbon atoms are joined together. (buzzine.com)
  • John Dalton represented compounds as aggregations of circular atoms, and although Johann Josef Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models. (wikipedia.org)
  • The concept of the chemical bond as a direct link between atoms can be modelled by linking balls (atoms) with sticks/rods (bonds). (wikipedia.org)
  • The models can be completed in any order, this helps free up the materials so that not all students are waiting to use the Carbon or Sodium atoms. (middleschoolscience.com)
  • His research focuses on the development and use of atomistic molecular dynamics and Monte Carlo simulation methods to study the thermodynamic and transport properties of materials, with special emphasis on ionic systems important in energy and environmental applications. (springer.com)
  • His research focuses on the development and application of atomistic molecular simulation methods to study the phase and interfacial behaviors of complex fluids. (springer.com)
  • 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)
  • To broaden the scope of this model, we propose the symmetry-adapted orbital model, which explicitly takes into account the level splittings of the electronic orbitals due to lower structural symmetries. (nature.com)
  • From the very early stages of structural studies of DNA by X-ray diffraction and biochemical means, molecular models such as the Watson-Crick nucleic acid double helix model were successfully employed to solve the 'puzzle' of DNA structure, and also find how the latter relates to its key functions in living cells. (wikipedia.org)
  • Structural information is generated from X-ray diffraction studies of oriented DNA fibers with the help of molecular models of DNA that are combined with crystallographic and mathematical analysis of the X-ray patterns. (wikipedia.org)
  • However, structural models coupled with biophysical and machine learning methods may be able to predict sequences that, when mutated, would be associated with more severe forms of OI. (mcponline.org)
  • To build appropriate structural models, we have applied a high throughput molecular dynamic approach. (mcponline.org)
  • Our models revealed structural differences that occur with different substituting amino acids. (mcponline.org)
  • In this study, we applied a molecular dynamics method to the analysis of the structural consequences of 57 disease-associated mutations in the α1(I) chain of type I collagen. (mcponline.org)
  • WHAT IF - a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. (bioinformatics.org)
  • We have focused on the violation of the spherical jellium model to extend the theory for the prediction of clusters. (nature.com)
  • An important challenge is how this information should be incorporated into statistical models for prediction of genetic values in animal and plant breeding programs or prediction of diseases. (genetics.org)
  • It is proved that the proposed SSCM strategy can remarkably improve the external prediction ability of QSAR models by employing two different datasets. (wiley.com)
  • MSMs for molecular kinetics are conceptually similar to our road-map example but instead of intersections, the states now correspond to basins in the free energy landscape governing the dynamics of the molecule. (bcr.org)
  • http://biotech.isCool.net or http://www.ahpcc.unm.edu/~aroberts or http://www.arc.unm.edu/~aroberts This site allows easy access to hyperlinks and free software for the biochemist, biophysicist and molecular biologist. (bio.net)
  • The Yale University cell and molecular biologist is probing the deep mysteries of epidermal cells. (the-scientist.com)
  • Quantum mechanical (QM) or molecular mechanical (MM) calculations to evaluate the importance of residues in and around active sites involving enzyme catalysis and combined QM/MM calculations to study enzymatic reactions. (nih.gov)
  • This model avoids excessive calculations of fluid-wall interactions and reduces the computational time drastically. (mdpi.com)
  • Investigations of the FLP reaction mechanisms were carried out using the transition state (TS) and the potential energy surface (PES) calculations plus the Born-Oppenheimer molecular dynamics (BOMD) as an efficient and robust implementation of general ab initio molecular dynamics scheme. (diva-portal.org)
  • To introduce students to molecular modelling techniques as applied to biological systems with particular emphasis on the methods used and their underlying theory. (warwick.ac.uk)
  • Molecular recognition is the basis of biological function. (bsc.es)
  • Computational models of chemical and biological systems at the atomic scale are an important tool for chemists. (energy.gov)
  • Our research focuses on the study of molecular recognition processes of biological significance from methodological and application points of view. (irbbarcelona.org)
  • Theoretical studies of small model systems of large biological impact. (irbbarcelona.org)
  • My research was driven by the theory that computer-based molecular modeling is useful in understanding the surface morphology, electrostatic potential, and reaction mechanisms of biological macromolecules. (scienceteacherprogram.org)
  • With the involvement of an increasing number of physicists in the field of mesocsopic modeling of molecular and cellular biological processes, huge progress has been accomplished in the two past decades. (cecam.org)
  • We discuss patterns and time-scales of ecological speciation identified by our model, and we highlight important parameters and features that need to be studied empirically in order to provide information that can be used to improve the biological realism and power of mathematical models of ecological speciation. (wiley.com)
  • This course is an extension of the course Molecular Modeling BB2280, and the aim is that the student should use the theoretical knowledge of BB2280 to solve a real chemical or biochemical problem. (kth.se)
  • The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. (elsevier.com)
  • Matt's expertise is specifically in the reconciliation of experimental and theoretical data to produce models that are indicative of actual, lab-scale behaviours and outcomes. (edu.au)
  • Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. (elsevier.com)
  • Discussing the advantages and disadvantages of various approaches, the authors develop a framework for identifying objectives, defining design parameters, measuring accuracy/accounting for error, validating and assessing various data collected, supporting software needs, and other requirements for planning a modeling project. (routledge.com)
  • Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. (elsevier.com)
  • There is a very wide range of approaches to physical modelling, and this article lists only the most common or historically important. (wikipedia.org)
  • MSMs for molecular kinetics have many advantages over other approaches. (bcr.org)
  • analytical approaches using mesoscopic models from the statistical physics , eventually coupled to hydrodynamics, elasticity, or electrostatics. (cecam.org)
  • These mechanistic approaches characterize the selective pressure by relying on an explicit model of the amino acid fitness landscape over the sequence. (umontreal.ca)
  • For this reason, the Bayesian least absolute shrinkage and selection operator (LASSO) (BL) appears to be an interesting approach for fitting marker effects in a regression model. (genetics.org)
  • Regressors include linear models (Bayesian ridge regression (BR) and linear regression with elastic net regularization (EN)), random forest (RF), kernel ridge regression (KRR) and two types of neural networks, graph convolutions (GC) and gated graph networks (GG). (google.com)
  • A molecular subtype of melanoma is loosely defined as those tumors containing the same set of molecular (primarily genetic) defect(s) and their associated pathways. (medindia.net)
  • Recent developments in our understanding of the molecular drivers of this disease have led to a new generation of targeted therapies that are proving effective in patients whose tumors harbor certain genetic defects. (medindia.net)
  • The information set now available for predicting genetic values may include, in addition to phenotypic records, a pedigree, molecular markers, or both. (genetics.org)
  • This chapter reviews depression assays involving acute stress (e.g., forced swim test), models consisting of prolonged physical or social stress (e.g., social defeat), models of secondary depression, genetic models, and experiments designed to elucidate the mechanisms of antidepressant action. (nih.gov)
  • Computational tools for analyzing the molecular consequences of genetic variation are of current interest because they have the potential to characterize the molecular pathogenesis for disease ( 1 - 3 ). (mcponline.org)
  • The model legume Lotus japonicus was demonstrated to be amenable to classical and molecular genetic analysis, providing the basis for the genetic dissection of the plant processes underlying nodulation and nitrogen fixation. (apsnet.org)
  • The results demonstrate that (i) Lotus japonicus is amenable to diploid genetic analysis, (ii) morphological and molecular markers segregate in true diploid fashion, (iii) molecular polymorphisms can be obtained at a reasonable frequency between the related Gifu and Funakura lines, and iv) the possibility exists for map-based cloning, marker assisted selection and mapping of symbiotic mutations through a genetic and molecular map. (apsnet.org)
  • Here we describe and study a stochastic, individual-based, explicit genetic model tailored for this palms system. (wiley.com)
  • 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)
  • As described by the jellium model, molecular orbitals generated by valence electrons in highly symmetric clusters have shapes just like atomic orbitals. (nature.com)
  • Molecular Modeling Techniques in Materials Science presents the background and tools for chemists and physicists to perform in-silico experiments to understand relationships between the properties of materials and the underlying atomic structure. (routledge.com)
  • The atomic and molecular orbital parts are represented by pastel/matte colored pieces and are color-coded according to their use. (sigmaaldrich.com)
  • The pink and purple pear-shaped lobes and concave pi links represent the +ve and -ve signs of the wave functions Ψ of the lobes of atomic and molecular orbitals. (sigmaaldrich.com)
  • Molray is a web interface to POV-Ray for producing high-quality molecular - graphics images from O plot files and other sources. (povray.org)
  • By developing and applying molecular simulation techniques to efficiently investigate these processes we aim at addressing open questions in pharmaceutical manufacturing and functional materials design. (ucl.ac.uk)
  • These models constitute pluggable modules that can be used to assemble comprehensive models of complex developmental processes. (rsc.org)
  • Molecular processes in nature affect human health, the availability of resources and the Earth s climate. (researchandmarkets.com)
  • This book will be of interest to graduate students and researchers looking to understand geochemical processes on a molecular level. (researchandmarkets.com)
  • Understand how quantum mechanical models can be used to describe chemical reactions and properties. (uio.no)
  • Mechanisms of reactions of the frustrated Lewis pairs (FLPs) with carbon dioxide (CO 2 ) and hydrogen (H 2 ) are studied by using quantum chemical modelling. (diva-portal.org)
  • we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. (osti.gov)
  • Molecular Modeling of Geochemical Reactions. (researchandmarkets.com)
  • Top quality Molymod molecular model sets are for use by students, teachers, and researchers. (sigmaaldrich.com)
  • Build custom model sets or upgrade your current sets with Molymod components. (sigmaaldrich.com)
  • The Molymod molecular orbital system uses standard shiny colored atom parts to represent the central atom cores. (sigmaaldrich.com)
  • Even for single models, the models are significantly more enriching than the template structure if the template is paralogous and shares more than 25% sequence identity with the target. (nih.gov)
  • Enrichment curves for the holo X-ray structure (black line), the apo X-ray structure (blue line), the consensus enrichment for multiple models (red line), and random selection (dotted line). (nih.gov)
  • For 8 targets (6 enzymes, one of which is a kinase, and 2 hormone receptors), enrichment curves are plotted for the holo X-ray structure (dotted line), the consensus based on multiple models (black line), and each single model (brown lines). (nih.gov)
  • In an effort to understand the role of the linker histone in chromatin folding, its structure and location in the nucleosome has been studied by molecular modeling methods. (nih.gov)
  • The structure of the globular domain of the rat histone H1d, a highly conserved part of the linker histone, built by homology modeling methods, revealed a three-helical bundle fold that could be described as a helix-turn-helix variant with its characteristic properties of binding to DNA at the major groove. (nih.gov)
  • Coordinate systems: how to describe 3-D molecular structure. (warwick.ac.uk)
  • Computer simulation and modeling have become powerful tools for understanding the structure and properties of a broad range of materials. (foresight.org)
  • Accordingly, a cluster will be stable when the number of valence electrons coincides with a closed-shell structure based on the jellium model. (nature.com)
  • The first reports of a double helix molecular model of B-DNA structure were made by James Watson and Francis Crick in 1953. (wikipedia.org)
  • How to Build a Model of the Molecular Structure of Graphite. (buzzine.com)
  • In this article, "molecular model" will primarily refer to systems containing more than one atom and where nuclear structure is neglected. (wikipedia.org)
  • The symmetrical arrangement of closely packed spheres informed theories of molecular structure in the late 1800s, and many theories of crystallography and solid state inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure. (wikipedia.org)
  • With this structure in hand, the researchers were then able to create a realistic in silico model of the cross-linking reaction. (cea.fr)
  • To estimate the tree structure for a set of taxa, we typically use a statistical model for evolution and compute the maximum likelihood estimate. (gerad.ca)
  • Computer model of the molecular structure of a crystal, used to demonstrate ideas on perspective. (sciencephoto.com)
  • This interactive tutorial explores how sound waves exhibit anisotropic character as a function of grain structure when traveling through a wooden block, which serves as an excellent model for the behavior of light passing through anisotropic crystals. (fsu.edu)
  • Christopher S. Anderson, Marta L. DeDiego, David J. Topham, and Juilee Thakar, "Boolean Modeling of Cellular and Molecular Pathways Involved in Influenza Infection," Computational and Mathematical Methods in Medicine , vol. 2016, Article ID 7686081, 11 pages, 2016. (hindawi.com)
  • To clarify their roles, and possible cross-talk, we have built a logical model for the nine key signalling pathways recurrently used in metazoan development. (rsc.org)
  • Moreover, these models of Drosophila pathways could serve as scaffolds for more complicated models of orthologous mammalian pathways. (rsc.org)
  • Comprehensive model annotations and GINsim files are provided for each of the nine considered pathways. (rsc.org)
  • The student must have started or completed the course Molecular Modeling BB2280. (kth.se)
  • This highly informative and carefully presented book comprises select proceedings of Foundation for Molecular Modelling and Simulation (FOMMS 2018). (springer.com)
  • The Lung Cancer model supplies doctors and their patients with a clear, high‐level guide to how tumor genetics can be leveraged to inform treatment decisions. (commerce.net)
  • Plant Molecular Genetics and Center for Legume Research, The University of Tennessee, Knoxville, TN 37901-1071 U.S.A. (apsnet.org)
  • These models could help computational biologists and drug development researchers understand and treat disease. (energy.gov)
  • Researchers then retrain the model on data from a different but related task. (energy.gov)
  • The MDMM is designed as an interface between the research and clinical communities where researchers can learn from clinical outcomes to refine molecular subtypes and clinicians can use the latest subtype information in treatment decisions. (medindia.net)
  • Especially useful to researchers doing molecular modeling … Nicely organized for readers who want to focus in quickly on a topic of interest. (routledge.com)
  • The first slate of lectures will be given from leading cancer researchers and oncologists who are familiar with multi-platform molecular and function imaging of cancer. (ismrm.org)
  • Y. V. Sergeev, S. Vitale, P. A. Sieving, A. Vincent, A. G. Robson, A. T. Moore, A. R. Webster and G. E. Holder: Molecular modeling indicates distinct classes of missense variants with mild and severe XLRS phenotypes. (nih.gov)
  • Various representations from the literature have been studied (Coulomb matrix, bag of bonds, BAML and ECFP4, molecular graphs (MG)), as well as newly developed distribution based variants including histograms of distances (HD), and angles (HDA/MARAD), and dihedrals (HDAD). (google.com)
  • The first part of the tutorial will provide a quick review of basic molecular simulation techniques. (google.com)
  • The Advanced Wooden Molecular Model Set is a kit that can be used for demonstrating both organic and inorganic and molecular geometry. (flinnsci.com)
  • Implemented using the logical modelling software GINsim , the resulting models qualitatively recapitulate the main characteristics of each pathway, in wild type as well as in various mutant situations ( e.g. loss-of-function or gain-of-function). (rsc.org)
  • Similar computational strategies can be used for the molecular modeling of a series of ligand:protein receptor interactions. (springer.com)
  • Molecular modeling indicates that the dimerization is promoted by interchain hydrophobic interactions between sections of alpha helix and beta helix. (nih.gov)
  • DNA molecular dynamics modeling involves simulating deoxyribonucleic acid (DNA) molecular geometry and topology changes with time as a result of both intra- and inter- molecular interactions of DNA. (wikipedia.org)
  • A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. (mdpi.com)
  • Note to faculty candidates: please include a note to the session chair during submission to alert them to your status*** +++Note: this session will be sorted jointly with Multiscale and Coarse-Grained Modeling of Polymers. (aiche.org)
  • HIFs were found to correlate with established RNA expression signatures, such as leukocyte infiltration, TGF-beta expression, IgG expression, and wound healing, and HIFs were shown to be predictive of molecular markers that are currently used for drug development clinical decision-making (PD-1, PD-L1, CTLA-4, TIGIT, and HRD) achieving AUROC ranging from 0.601 to 0.864 in held-out tissue source sites. (prweb.com)
  • Results indicate that inclusion of markers in the regression further improved the predictive ability of models. (genetics.org)
  • A theory with such "predictive power," as Newton calls it, could serve as a basis for designing molecular systems to improve upon photosynthesis and energy production in general. (bnl.gov)
  • Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. (osti.gov)
  • In future, the proposed SSCM strategy may provide a new direction to develop more accurate predictive models. (wiley.com)
  • These paradigms are critically evaluated in relation to their ease, validity and replicability, the molecular insights that they have provided, and their capacity to offer the next generation of therapeutics for depression. (nih.gov)
  • Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible. (researchandmarkets.com)
  • Volume 2: In Vivo Models, Imaging, and Molecular Regulators contains today's best protocols for classifying tumors into response categories and for customizing therapy to individuals. (worldcat.org)
  • These techniques allow measurements of DNA damage, apoptotic cell death, and the molecular and cellular regulators of cytotoxicity, as well as in vivo animal modeling of chemosensitivity. (worldcat.org)
  • Topics of interest include, but are not limited to, development of new modeling and simulation techniques, application of modeling and simulation to provide insight into the properties and behavior of polymeric materials, and the development and use of multiscale techniques for polymeric materials. (aiche.org)
  • the first of these, The Targeted Therapy Finder - Melanoma, leverages the MDMM to find treatments targeted to a patient's specific molecular profile. (medindia.net)
  • In providing financial support for this important open-science initiative, we are aiming to help physicians and patients understand the therapeutic options that best fit the patient's molecular profile, with the goal of delivering more effective, personalized care. (commerce.net)
  • Using Drosophila as a model of FXS, we showed that select expression of dfmr1 in the insulin-producing cells (IPCs) of the brain was sufficient to restore normal circadian behavior and to rescue the memory deficits in the fragile X mutant fly. (nature.com)
  • Our results indicate that insulin misregulation underlies the circadian and cognitive phenotypes displayed by the Drosophila fragile X model, and thus reveal a metabolic pathway that can be targeted by new and already approved drugs to treat fragile X patients. (nature.com)
  • To better understand disease pathogenesis, we use a Drosophila fragile X model, based on loss of dfmr1 function, which displays several relevant phenotypes, including defects in the circadian output pathway, memory in the conditioned courtship and olfactory conditioning paradigms, social interaction (with peers and in naïve courtship) and neural development. (nature.com)
  • Notably, the mGluR pathway has been shown to be misregulated in both mouse and fly models of FXS, and, importantly, treatment with mGluR inhibitors rescues memory and other phenotypes in both Drosophila and mammalian models of the disease. (nature.com)
  • In this thesis, we describe a quantitative, mechanistic model of electroporation and concomitant molecular transport that can be used for guiding and interpreting electroporation experiments and applications. (mit.edu)
  • Our research is focused on the application of molecular simulation methods to tackle problems in the fields of chemical and biochemical engineering. (ucl.ac.uk)
  • Cancer Commons, an initiative of CollabRx, a provider of information technology to personalize cancer treatments and accelerate research, announces the publication of a molecular disease model of melanoma (MDMM) which classifies the disease into molecular subtypes, rather than traditional histological or cellular subtypes, and describes treatment guidelines for each subtype, including specific assays, drugs, and clinical trials. (medindia.net)
  • PALO ALTO, Calif.-(BUSINESS WIRE)-Cancer Commons, an open‐science initiative to personalize cancer treatments and accelerate research, announces the publication of a molecular disease model (MDM) for lung cancer. (commerce.net)
  • The Institute for Sustainability and Innovation has boosted its molecular modelling capability with the employment of post-doctoral research fellow Dr Matthew Stewart. (edu.au)
  • His research group is also active in the development of free-energy-based molecular simulation methods for computing the interfacial properties of model systems. (springer.com)
  • Novice practitioners of molecular modelling, experienced computational chemists, and experimentalists seeking to understand this field will all find information and knowledge of use in their research. (researchandmarkets.com)
  • The MDMM consists of a set of "actionable" molecular subtypes and proposed practice guidelines for treating each subtype: which therapies (approved or experimental) should be considered and which are contraindicated. (medindia.net)
  • The model predictions of molecular uptake are in excellent agreement with these experimental measurements, for which the applied electric pulses collectively span nearly three orders of magnitude in pulse duration (50 ts -20 ms) and an order of magnitude in pulse magnitude (0.3 -3 kV/cm). (mit.edu)
  • These findings indicate that ML models could be more accurate than DFT if explicitly electron correlated quantum (or experimental) data was provided. (google.com)
  • This review addresses the mechanisms which are thought to be involved in OA pain, derived from studies on pain mechanisms in humans and in experimental models of OA. (frontiersin.org)
  • MSMs for molecular kinetics, however, must be inferred from simulation trajectories (like molecular dynamics trajectories). (bcr.org)
  • The student will need to find and present a chemical or biochemical problem that can be studied using different molecular modeling techniques. (kth.se)
  • The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction is molecular graphics, but these topics are closely linked and each uses techniques from the others. (wikipedia.org)
  • Case studies and mathematical models of ecological speciation. (wiley.com)
  • In such clusters, the validity of the spherical jellium model decreases relatively due to the split and shift of the superatomic orbital levels. (nature.com)
  • To account for the variation in the ligand-binding pocket as it binds different ligands, we calculate "consensus" enrichment by ranking each library compound by its best docking score against all available comparative models and/or modeling templates. (nih.gov)
  • We show that these methods give insight into the underlying adsorption mechanisms of pure components in model DNCs and that the application of these methods can be extended to mixtures and used to develop design criteria for new materials with improved separations capabilities. (aiche.org)
  • PathAI developed a machine learning (ML) model-based pipeline to predict tumor molecular phenotypes from hematoxylin and eosin (H&E) stained biopsies across 5 different tumor types. (prweb.com)
  • Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes. (prweb.com)
  • An advantage of explicitly regressing phenotypes on marker covariates is that the model can produce information about genomic regions that may affect the trait of interest. (genetics.org)
  • The goal with this course is to provide an overview of the methods and techniques which are used within modern molecular modeling. (kth.se)
  • The book presents information on how to handle different materials and how to choose an appropriate modeling method or combination of techniques to better predict material behavior and pinpoint effective solutions. (routledge.com)
  • These representations include closely packed spheres (CPK models) made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. (wikipedia.org)