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)

Molecular design software Molecular graphics Molecular modelling Ribbon diagram Software for molecular mechanics modeling Space ... The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their ... "Molecular Models - Tangible Representations of the Abstract". PDB Newsletter. 41: 4-5. [1] history of molecular models Paper ... A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an ...
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The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and ...
... which performs common tasks in molecular modelling. The Molecular Modeling Toolkit is a library that implements common ... Konrad Hinsen, The Molecular Modeling Toolkit: A New Approach to Molecular Simulations As of 28 April 2011[update], MMTK ... "The Molecular Modeling Toolkit: A New Approach to Molecular Simulations". J. Comput. Chem. 21 (2): 79-85. doi:10.1002/(SICI) ... Molecular modelling software, Molecular dynamics software, Python (programming language) software, All stub articles, ...
Molecular modeling of RNA polymerase. Molecular modeling of a bacterial DNA primase template. Molecular modeling of DNA ... Molecular modeling of DNA repair Animated skeletal model of A-DNA. Simplified models of chromatin. Simplified model of ... The DNA model shown (far right) is a space-filling, or CPK, model of the DNA double helix. Animated molecular models, such as ... DNA spacefilling molecular model A model of a designed DNA tetrahedron. 15 m long DNA model, Naturalis Biodiversity Center ...
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA ... Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics) are ... Molecular modelling, Computational chemistry, Molecular dynamics, Chemistry software, GPGPU). ... and molecular mechanics Blaze ligand-based virtual screening CHARMM - Molecular dynamics [1] CP2K Ab initio molecular dynamics ...
... physics List of software for Monte Carlo molecular modeling Software for molecular mechanics modeling Bond fluctuation model ... Monte Carlo molecular modelling is the application of Monte Carlo methods to molecular problems. These problems can also be ... Molecular modelling, Theoretical chemistry, Monte Carlo methods, Stochastic models). ... modelled by the molecular dynamics method. The difference is that this approach relies on equilibrium statistical mechanics ...
... molecular modeling List of software for nanostructures modeling Molecular design software Molecular dynamics Molecular modeling ... Molecular dynamics software, Molecular modelling software, Science software). ... Resources Short list of Molecular Modeling resources OpenScience Biological Magnetic Resonance Data Bank Materials modelling ... This is a list of computer programs that are predominantly used for molecular mechanics calculations. GPU - GPU accelerated I ...
Molecular modelling software, Monte Carlo molecular modelling software). ... This is a list of computer programs that use Monte Carlo methods for molecular modeling. Abalone classical Hybrid MC BOSS ... software Comparison of software for molecular mechanics modeling Comparison of nucleic acid simulation software Molecular ... Towhee) (16 September 2013). "MCCCS Towhee: a tool for Monte Carlo molecular simulation". Molecular Simulation. 39 (14-15): ...
German chemist August Wilhelm von Hofmann was the first to make stick-and-ball molecular models, which he used in lecture at ... which clearly show both semi-correct molecular geometries, such as a linear water molecule, and correct molecular formulas, ... corresponds to the relationship between respective molecular weights. Hence, relative molecular masses could now be calculated ... In chemistry, the history of molecular theory traces the origins of the concept or idea of the existence of strong chemical ...
Model., 2007, 47, 295-301. doi:10.1021/ci600305h SMARTS International Chemical Identifier Java Webstart application for MQL ( ... The Molecular Query Language (MQL) was designed to allow more complex, problem-specific search methods in chemoinformatics. In ... E. Proschak, J. K. Wegner, A. Schüller, G. Schneider, U. Fechner, Molecular Query Language (MQL)-A Context-Free Grammar for ...
... molecular mechanics and dynamics; peptide modeling; structural biology; cheminformatics and QSAR. Molecular modeling and ... Molecular modeling, molecular docking, and MD simulations are some of many computation studies that takes places during drug ... protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific ... molecular modeling, and computer-driven molecular design. Researchers specializing in pharmaceutics (drug-discovery); ...
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. ... 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 ...
Springs are cross-linked to represent mechanical behavior of the material and bridge molecular dynamics (MD) model and finite ... The Gaussian network model is a minimalist, coarse-grained approach to study biological molecules. In the model, proteins are ... Another model for protein dynamics based on elastic mass-and-spring networks is the Anisotropic Network Model. The Gaussian ... The model uses the harmonic approximation to model interactions. This coarse-grained representation makes the calculations ...
Molecular Physics. 118 (9-10). van der Giessen, Erik (March 2020). "Roadmap on multiscale materials modeling". Modelling and ... OpenKIM has been directly integrated into various prominent molecular modelling and potential fitting software including LAMMPS ... A key aspect of OpenKIM is that in addition to model parameters, it also stores the complete source code of "portable models" ... ASE, DL_POLY, GULP, and potfit, and is recognized in the molecular modelling community as being a critical step towards ...
... in contrast to continuum models. These models generally occur in the application of molecular mechanics (MM) and dynamics (MD) ... These models can make useful contributions when the solvent being modelled can be modelled by a single function i.e. it is not ... Solvation Models (SMx) and the Solvation Model based on Density (SMD) have also seen wide spread use. SMx models (where x is an ... The Polarizable continuum model (PCM) is a commonly used implicit model and has seeded the birth of several variants. The model ...
Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of ... Hadley KR, McCabe C (July 2012). "Coarse-Grained Molecular Models of Water: A Review". Molecular Simulation. 38 (8-9): 671-681 ... Coarse-grained models have found practical applications in molecular dynamics simulations. Another case of interest is the ... An example is given by the chemomechanical dynamics of a molecular machine, such as Kinesin. The coarse-grained modeling ...
"Revisiting the Paraquat-Induced Sporadic Parkinson's Disease-Like Model". Molecular Neurobiology. 56 (2): 1044-1055. doi: ... Parkinson's disease animal models are divided into two categories: neurotoxin models and genetic models. Neurotoxin models ... The pre-formed fibril model was developed as a way to study the propagation of α-synuclein. This model consists of injecting ... A limitation to the pre-formed fibril model is that although it is a widely used model, it lacks overt neurodegeneration. The ...
Molecular markers provide only a "sample" of the genetic information in which to compare individuals of populations, and can ... The SMM is distinguished from the Kimura-Crow model, also known as the infinite alleles model (IAM), in that as the population ... The original model assumes that if an allele has a mutation that causes it to change in state, mutations that occur in ... The SMM model takes into account the frequency of mismatches between microsatellite loci, meaning the number of times there are ...
Methods in Molecular Biology. Vol. 1727. pp. 343-352. doi:10.1007/978-1-4939-7571-6_25. ISBN 978-1-4939-7570-9. ISSN 1940-6029 ... As current models are highly reliant on FAD mutations to induce Alzheimer's like pathology, there is still no ideal model that ... While these models are useful in studying the process of aging, they are not always exact models of Alzheimer's disease. Common ... Experimental models of Alzheimer's disease are organism or cellular models used in research to investigate biological questions ...
Molecular Metabolism. 32: 27-43. doi:10.1016/j.molmet.2019.11.010. ISSN 2212-8778. PMC 6938849. PMID 32029228. Hall, K. D. ( ... Taubes, Gary (2022). "The energy balance model compared with the carbohydrate-insulin model". The American Journal of Clinical ... The carbohydrate-insulin model (CIM) posits that obesity is caused by excess consumption of carbohydrate, which then disrupts ... It is contrasted with the mainstream energy balance model (EBM), which holds that obesity is caused by a excess in calorie ...
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 - ...
This means that even a model that can account for a vast number of molecular species and reactions is not necessarily ... SRSim is integrated in the LAMMPS molecular dynamics simulator and allows the user to specify the model in BNGL. SRSim allows ... Monod J, Wyman J, Changeux JP (May 1965). "On the nature of allosteric transitions: A plausible model". Journal of Molecular ... Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite ...
"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 of special issues of J. Phys. ... Her Ph.D. research at the Fritz Haber Center focused on molecular dynamics in rare gas clusters and matrices. Upon completing ... Krylov has also contributed to the development of molecular orbital concepts in the framework of many-body wave functions and ...
Molecular Microbiology. 44 (6): 1575-87. doi:10.1046/j.1365-2958.2002.02978.x. PMID 12067345. S2CID 42229269. SWISS-MODEL. ... Matched templates Model report Other data Dimethyl+sulfide:cytochrome+c2+reductase at the U.S. National Library of Medicine ... McDevitt CA, Hugenholtz P, Hanson GR, McEwan AG (June 2002). "Molecular analysis of dimethyl sulphide dehydrogenase from ...
This means models can be generated based upon molecular lesions consistent with the human disease. Metastasis is a process of ... Mice may not be an ideal model for breast cancer. This is mainly due to the lack of precision in many of the models. When ... 2003). Models of Breast Cancer: quo vadis, animal modeling? Breast Cancer Research 6(31), 31-38.doi: 10.1186/bcr723 Pulaski BA ... For a list of other mammary gland specific promoters and mouse models see. MMTV-PyMT is the model of breast cancer metastasis, ...
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 ...
Molecular Psychiatry. 9 (9): 833-845. doi:10.1038/sj.mp.4001529. PMID 15184908. Institute of Medicine (2004). Immunization ... Klauck, S. M.; Poustka, A. (2006). "Animal models of autism". Drug Discovery Today: Disease Models. 3 (4): 313-318. doi:10.1016 ... researchers often focus only on single features of autism when using animal models. One of the more common rodent models is the ... "Animal Models of Autism". Transgenic and Knockout Models of Neuropsychiatric Disorders. Contemporary Clinical Neuroscience. p. ...
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". ...
Agronomy, Molecular biology) Populus, genus used as a model in forest genetics and woody plant studies. It has a small genome ... Lotus japonicus, model legume used to study the symbiosis responsible for nitrogen fixation. (Agronomy, Molecular biology) ... Genetics, Molecular biology, Agronomy) Medicago truncatula, model legume, closely related to the common alfalfa. Its rather ... Agronomy, Molecular biology) Mimulus guttatus, model organism used in evolutionary and functional genomes studies. The genus ...
Molecular design software Molecular graphics Molecular modelling Ribbon diagram Software for molecular mechanics modeling Space ... The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their ... "Molecular Models - Tangible Representations of the Abstract". PDB Newsletter. 41: 4-5. [1] history of molecular models Paper ... A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an ...
Molecular Model of Prion Transmission to Humans. Emerging Infectious Diseases. 2009;15(12):2013-2016. doi:10.3201/ ... Jones, M., Wight, D., Barron, R., Jeffrey, M., Manson, J. C., Prowse, C....Head, M. W. (2009). Molecular Model of Prion ... Molecular Model of Prion Transmission to Humans. Volume 15, Number 12-December 2009 ... Molecular analysis of prion strain variation and the aetiology of new variant CJD. Nature. 1996;383:685-90. DOIPubMedGoogle ...
The discovery of the structure of DNA by Francis Crick and James Watson in the early 1950s ushered in a new era in molecular ... Brief Overview of Molecular Biology and Cancer Brief Overview of Molecular Biology and Cancer. The discovery of the structure ... This ability has led to one particular model of oral cancer development, field cancerization. In this model, not only is the ... Cellular and Molecular Interactions. Overall, the genetics behind carcinoma in the head and neck region are complex [11] ; ...
Specifically, techniques such as domain identification, homology modeling, in silico drug screening, and pharmacophore ...
You can simulate molecular flow, such as rarefied gas flows in vacuum systems, in COMSOL Multiphysics®. See examples and gain ... You can simulate molecular flow, such as rarefied gas flows in vacuum systems, in COMSOL Multiphysics®. See examples and gain ... The new Molecular Flow Module provides vacuum engineers with previously unavailable tools for modeling gas flows within vacuum ... What Is Molecular Flow?. April 16, 2013. Vacuum is naturally associated with the hostile environment of deep space. To achieve ...
The model of ICAM-1 and LFA-1 molecular interaction was used to test the application of the Molecular Recognition Theory for ... The model of ICAM-1 and LFA-1 molecular interaction was used to test the application of the. Molecular Recognition Theory for ... "Modelling of ICAM-1 and LFA-1 Interaction Using Molecular Recognition Theory." Croatica Chemica Acta, vol. 81, br. 2, 2008, str ... "Modelling of ICAM-1 and LFA-1 Interaction Using Molecular Recognition Theory." Croatica Chemica Acta 81, br. 2 (2008): 283-287 ...
The molecular biology models are built with quality materials that wont degrade even after multiple constructions, alterations ... molecular biology models support visual learning in the classroom. The replicas showcase hydrogen bonds in DNA, covalent ... Visualize and Understand How Elements Combine to Form CompoundsTransferring DNA and molecular bond images into three- ... Basic Molecular Models Student Activity Models Molecular Biology Models Visualize and Understand How Elements Combine to Form ...
Molecular Modelling Analysis of the Metabolism of Zaleplon ... Molecular Modelling Analysis of the Metabolism of Zaleplon ... Molecular Modelling Analysis of the Metabolism of Zaleplon. Journal of Pharmacology and Toxicology, 1: 328-336. DOI: 10.3923/ ... Molecular modelling analysis of the antioxidant activity of probucol. Asian J. Biochem., 2: 354-358.. CrossRefDirect Link. ... Molecular modelling analyses of the metabolism of clofarabine. J. Pharmacol. Toxicol., 2: 599-609.. CrossRefDirect Link. ...
Various molecular vibration models were examined: perfect gas, one-temperature model (equilibrium), and two-temperature model ( ... One-temperature and two-temperature models predicted very similar surface conditions for the blunt-body. ... This paper discusses modeling of molecular vibration in thermal nonequilibrium airflow. The effects of high-temperature ... Various molecular vibration models were examined: perfect gas, one-temperature model (equilibrium), and two-temperature model ( ...
Interactions of ionic liquids and their mixtures with carbon nanomaterials: insights from molecular modeling ... insights from molecular modeling. Abstracts of papers - American Chemical Society, 242. -. ISSN 0065-7727 ...
Neurotransmitter homeostasis in and around a synapse involves complex random processes such as diffusion, molecular binding, ... Molecular Diffusion Model of Neurotransmitter Homeostasis Around Synapses Supporting Gradients In Special Collection: CogNet ... Ashwin Mohan, Sandeep Pendyam, Peter W. Kalivas, Satish S. Nair; Molecular Diffusion Model of Neurotransmitter Homeostasis ... A three-dimensional stochastic diffusion model of a synapse was developed to provide molecular-level details of ...
... molecular epidemiology, exposure and risk assessments, family studies, genomic studies, metabolomics, and microbiomics. ... Absolute Risk Modeling. DCEG investigators in the Biostatistics Branch have developed models (such as the Gail model) for ... Molecular Epidemiology. We use molecular epidemiology to examine the relationship of genetic and environmental risk factors to ... These models have been used to counsel individual patients on their disease risk; to make more formal management ...
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... band Hubbard model is not valid. In this interesting regime intriguing quantum phenomena appear due to the interplay between ... 42nd Annual Meeting of the APS Division of Atomic, Molecular and Optical Physics Volume 56, Number 5. Monday-Friday, June 13-17 ...
Molecular Modeling Techniques and In-Silico Drug Discovery. Bagchi, Angshuman. Afiliação *Bagchi A; Department of Biochemistry ... Molecular modeling is the technique to determine the overall structure of an unknown molecule, be it a small one or a ... Molecular Modeling Techniques and In-Silico Drug Discovery. ... an overview of the protocol associated with molecular modeling ... Desenho de Fármacos; Descoberta de Drogas; Simulação de Acoplamento Molecular; Modelos Moleculares; Descoberta de Drogas/ ...
Launch of Nostrum BioDiscovery, a spin-off that applies supercomputing to speed up drug ...
Launch of Nostrum BioDiscovery, a spin-off that applies supercomputing to speed up drug ...
Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 46​, 9052 Zwijnaarde, ... A systematic molecular level and spectroscopic investigation is presented to show the cooperative role of Brønsted acid and ... Light Olefin Diffusion during the MTO Process on H-SAPO-34: a Complex Interplay of Molecular Factors. ... Enhanced sampling molecular dynamics simulations based on either force fields or density functional theory are used to ...
Operational Model Calculations.. Concentration-response curves of both functional assays were fitted to the operational model ( ... 2000) Molecular cloning and characterization of a new human histamine receptor, HH4R. Biochem Biophys Res Commun 279:615-620. ... 1983) Operational models of pharmacological agonism. Proc R Soc Lond B Biol Sci 220:141-162. ... Your Name) has forwarded a page to you from Molecular Pharmacology Message Body (Your Name) thought you would be interested in ...
The potential of molecular imaging lies in the fact that detected disease-specific molecules can be used both as diagnostic and ... The potential of molecular imaging lies in the fact that detected disease-specific molecules can be used both as diagnostic and ... To date, anti-VEGF PET studies were conducted in a glioblastoma rat model to evaluate the ability of anti-VEGF antibodies to ... Molecular imaging represents a novel and growing medical discipline that enables the visualization, characterization, and ...
Demonstrate knowledge of bonding models. *Use knowledge of molecular forces to explain bulk properties of matter ... Molecular Architecture is an introduction to university chemistry with an emphasis on relating bulk properties to molecular ... architecture and determining molecular structure. It consists of five lecture modules and a laboratory course. ...
Home/ Collections/ Mid-Century Molecular Structure Model In yellow. Mid-Century Molecular Structure Model In yellow. ₩760,000 ...
Luce Micaela Mattio Post Doc Molecular Modeling and Drug Discovery Enrico Bergamaschi Post Doc Molecular Modeling and Drug ... Marco Borgogno Affiliated Researcher Molecular Modeling and Drug Discovery Mara Di Filippo Post Doc Molecular Modeling and Drug ... Manuel Jose Ruiz Munevar PhD Student Fellow Molecular Modeling and Drug Discovery ...
This is the molecular structure of theobromine, you may know it as chocolate! Although pictured here stitched in black you ... Molecular model - Theobromine (otherwise known as chocolate!). Regular price £6.50 Sale price £0.00 Unit price /per ... Home › Molecular model - Theobromine (otherwise known as chocolate!) #ProductImage-35523999465634 { max-width: 700px; max- ... This is the molecular structure of theobromine, you may know it as chocolate! ...
Large Language Models can make mistakes. Consider checking important information. Im OK to proceed. ... Church, the Molecular and Pediatric Pathologist at Boston Childrens Hospital, talks to NewsMedical about their work in ... Nelson have discovered the molecular mechanism that inhibits HCV replication in vitro after its host cells become crowded and ... can inhibit replication by depriving viral agents of their molecular building blocks. However, those therapies may impact ...
Read more about Modelling the health of Caribbean coral reefs - a glimmer of hope? ...
Application of a quality management system model for laboratory services; approved guideline, 3rd ed. Wayne, PA: Clinical and ... Molecular Genetic Test Reports. Content. Molecular genetic test reports must comply with the CLIA general test report ... Considerations Before Introducing Molecular Genetic Testing or Offering New Molecular Genetic Tests Recommendations described ... considerations before introducing molecular genetic testing or offering new molecular genetic tests,and the quality management ...
The discovery of the structure of DNA by Francis Crick and James Watson in the early 1950s ushered in a new era in molecular ... Brief Overview of Molecular Biology and Cancer Brief Overview of Molecular Biology and Cancer. The discovery of the structure ... This ability has led to one particular model of oral cancer development, field cancerization. In this model, not only is the ... Cellular and Molecular Interactions. Overall, the genetics behind carcinoma in the head and neck region are complex [8] ; ...
In Vivo Activity of Combined PI3K/mTOR and MEK Inhibition in a KrasG12D;Pten Deletion Mouse Model of Ovarian Cancer ... Molecular and Biologic Analysis of Histone Deacetylase Inhibitors with Diverse Specificities Andrea Newbold, Geoffrey M. ... Open the PDF for Preclinical Evaluation of Nilotinib Efficacy in an Imatinib-Resistant KIT-Driven Tumor Model in another window ... Open the PDF for Molecular and Biologic Analysis of Histone Deacetylase Inhibitors with Diverse Specificities in another window ...
  • Some modeling analyses suggest 5 separate events are required in colon cancer. (medscape.com)
  • However, in order to achieve better efficiency this heuristic algorithm of molecular recognition has to be combined to several other procedures: molecular hydropathy analyses, secondary structure prediction methods and protein database search. (srce.hr)
  • Molecular modelling analyses of the metabolism of clofarabine. (scialert.net)
  • To achieve these goals, the consensus principal component analysis (CPCA) technique and distance measurements were used to explore available crystal structures, newly built homology models, and repeated molecular dynamics simulations. (aspetjournals.org)
  • The application of molecular dynamics simulations to highly flexible proteins such as cytochromes P450 is also explored and the information is extracted by the CPCA. (aspetjournals.org)
  • MD, molecular dynamics. (aspetjournals.org)
  • Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. (aip.org)
  • The differences in physical properties between the outer and inner leaflets of mouse hepatocyte cell membrane models were investigated by performing 1.2 μ s-long all-atomistic molecular dynamics calculations under physiological temperature and pressure conditions (310.15 K and 1 atm). (aip.org)
  • We do research into two complementary approaches: First, algorithms to infer interpretable and physically consistent mathematical models that are sufficient to describe observed dynamics. (mpi-cbg.de)
  • The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected. (wikipedia.org)
  • 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 embedded magnets in the atoms reflect the correct positive or negative charges to give students hands-on experience in molecular attraction or repulsion. (flinnsci.com)
  • The Molecular Model allowed students to visualize the bonds between differing atoms. (northwestern.edu)
  • The Unit molecular system features large (44mm diameter) spheres in seven colours to represent different atoms and 25mm diameter white spheres representing hydrogen atoms joined by a versatile peg system. (cochranes.co.uk)
  • Available as a large demonstration set, with either metal or plastic bonds or packs of individual atoms, pegs, accessories and rigid and flexible bonds for making custom molecular models. (cochranes.co.uk)
  • This work had two separate aims: to evaluate different modeling techniques and to make a detailed structural characterization of CYP2C9. (aspetjournals.org)
  • Molecular cytogenetic profiling of canine HS in these breeds would serve to reveal recurrent DNA copy number aberrations (CNAs) that are breed and/or tumor associated, as well as defining those shared with human HS. (biomedcentral.com)
  • Genetic testing encompasses a broad range of laboratory tests performed to analyze DNA, RNA, chromosomes, proteins, and certain metabolites using biochemical, cytogenetic, or molecular methods or a combination of these methods. (cdc.gov)
  • Presenter Petr Šulc, Arizona State University Petr Šulc's research focuses on application of computational modeling and statistical physics approaches to complex systems. (foresight.org)
  • In particular, his group uses computational models to study problems in biology, and bio-inspired nanotechnology systems. (foresight.org)
  • The first ball-and-peg models to help students visualize molecules in 3D was conceptualized by Professor Charles Hurd . (northwestern.edu)
  • Specifically, techniques such as domain identification, homology modeling, in silico drug screening, and pharmacophore identification allow us to develop a greater understanding of the potential roles of these proteins in signal transduction and gene expression. (mdpi.com)
  • Tapping into both AlphaFold and RoseTTAFold, they tweaked the programs to predict which proteins are likely to tag-team and sketched up the resulting complexes into a 3D models. (singularityhub.com)
  • The CPCA was based on molecular interaction fields focused on the active site regions of the proteins and include detailed amino acid analysis. (aspetjournals.org)
  • Cross homology models of CYP2C9 and CYP2C5, using their respective crystal structures as templates, indicated that such models were more similar to their templates than to their target proteins. (aspetjournals.org)
  • A molecular model is a physical model of an atomistic system that represents molecules and their processes. (wikipedia.org)
  • However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models. (wikipedia.org)
  • The model of ICAM-1 and LFA-1 molecular interaction was used to test the application of the Molecular Recognition Theory for the identification of several discontinuous binding regions, i.e. ligand-receptor sites, within large antigenic molecules. (srce.hr)
  • Molecular Recognition Theory is an applicable heuristic algorithm for identification of possibly interacting amino acid pairs in short linear epitope/paratope sites within larger molecules. (srce.hr)
  • Our simulations help unravel the molecular mechanisms of tissue formation across scales, from molecules to organism. (mpi-cbg.de)
  • The breed associated clinical features and DNA copy number aberrations exhibited by canine HS offer a valuable model for the human counterpart, providing additional evidence towards elucidation of the pathophysiological and genetic mechanisms associated with histiocytic malignancies. (biomedcentral.com)
  • If the simulated mechanisms are sufficient to bring about the experimentally observed behavior, we can further leverage the power of experimental data to predict minimal necessary models. (mpi-cbg.de)
  • In addition to predictive simulations and data-driven models, reverse-engineering the molecular mechanisms of tissue formation also requires direct comparison with microscopy images and a healthy portion of biological and biophysical intuition in order to come up with novel hypotheses. (mpi-cbg.de)
  • The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. (wikipedia.org)
  • Molecular pathways of pulmonary inflammation following aspiration and inhalation of stainless steel welding fume in mice. (cdc.gov)
  • The recognition of cancer as a heterogeneous disease, coupled with technological advances in molecular/genomic profiling of tumors, provides epidemiologists with the opportunity to integrate tissue profiling in etiologic studies to study the carcinogenesis process, and pinpoint specific factors associated with risk for developing specific molecular or genomic cancer subtypes. (cancer.gov)
  • Biomolecular simulations Research in the Chong lab involves the development and application of molecular simulation approaches to model a variety of biophysical processes. (foresight.org)
  • In addition, we work on Lagrangian methods for simulations on moving and deforming geometries , on solving vector- and tensor-valued equation models of active matter on dynamic 3D surfaces, and on increasing the numerical accuracy of simulations using a novel approach to polynomial interpolation problems. (mpi-cbg.de)
  • It also allows us to merge data-driven and model-driven approaches, e.g., using machine learning surrogates to accelerate numerical simulations or to use numerical theory to constrain the training of machine-learning methods for guaranteed consistency. (mpi-cbg.de)
  • There is a very wide range of approaches to physical modeling, including ball-and-stick models available for purchase commercially, to molecular models created using 3D printers. (wikipedia.org)
  • We focus on approaches that combine principled knowledge of numerical algorithms with modern machine learning models. (mpi-cbg.de)
  • Molecular modeling of the Jak3 kinase domains and structural basis for severe combined immunodeficiency. (medlineplus.gov)
  • 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)
  • Symmetrical comparative modeling on fibrillar template is run through the RosettaCM protocol of Rosetta. (lu.se)
  • p21 and other tumor suppressor genes' inactivation are therefore most likely involved in the first steps of the cancer model, with later stages possibly involving protooncogene activation and inflammation. (medscape.com)
  • These findings indicate that certain prostate cancer cells are dependent on MUC1-C for growth and survival and that directly targeting MUC1-C results in their death in vitro and in tumor models. (aacrjournals.org)
  • The course covers theoretical models for the structure and reactions of atomic nuclear, as well as experiments in nuclear physics and their scientific applications. (lu.se)
  • 2008). 'Modelling of ICAM-1 and LFA-1 Interaction Using Molecular Recognition Theory', Croatica Chemica Acta , 81(2), str. (srce.hr)
  • Štambuk N, Konjevoda P, Vikić-Topić D, Pokrić B. Modelling of ICAM-1 and LFA-1 Interaction Using Molecular Recognition Theory. (srce.hr)
  • By comparing simulation and experimental results, we validated our models and obtained insights into the mAbs' self-interaction properties, highlighting the role of both ion binding and charged patches on the mAb surfaces. (lu.se)
  • Our models provide useful information about mAbs' self-interaction properties and can assist the screening of conditions driving to colloidal stability. (lu.se)
  • If distinct conformers and glycotypes of PrP d are responsible for diversity of prion strains, then they would be expected to be able to impose these molecular characteristics onto PrP C of the same amino acid sequence (when transmitted or replicating within a species) and onto PrP C of a different primary sequence (when transmitted between species). (cdc.gov)
  • We have previously reported that the molecular characteristics, electrophoretic mobility, and glycoform ratio of the PrP res associated with the vCJD PrP d conformer were faithfully reproduced by PMCA ( 10 ). (cdc.gov)
  • The multihit model postulates that several unique genetic mutations combine to cause cancer. (medscape.com)
  • We use molecular epidemiology to examine the relationship of genetic and environmental risk factors to cancer etiology. (cancer.gov)
  • DCEG investigators are also undertaking foundational research to identify novel molecular and genomic signatures in tumors linked to germline genetic variants and certain environmental exposures. (cancer.gov)
  • Laboratories that perform molecular genetic testing are subject to the general CLIA quality systems requirements for nonwaived testing and the CLIA personnel requirements for tests of high complexity. (cdc.gov)
  • Although many laboratories that perform molecular genetic testing comply with applicable regulatory requirements and adhere to professional practice guidelines,specific guidelines for quality assurance are needed to ensure the quality of test performance. (cdc.gov)
  • To enhance the oversight of genetic testing under the CLIA framework,CDC and the Centers for Medicare & Medicaid Services (CMS) have taken practical steps to address the quality management concerns in molecular genetic testing,including working with the Clinical Laboratory Improvement Advisory Committee (CLIAC). (cdc.gov)
  • This report provides CLIAC recommendations for good laboratory practices for ensuring the quality of molecular genetic testing for heritable diseases and conditions. (cdc.gov)
  • The recommended practices address the total testing process (including the preanalytic,analytic,and postanalytic phases),laboratory responsibilities regarding authorized persons,confidentiality of patient information,personnel competency,considerations before introducing molecular genetic testing or offering new molecular genetic tests,and the quality management system approach to molecular genetic testing. (cdc.gov)
  • These recommendations are intended for laboratories that perform molecular genetic testing for heritable diseases and conditions and for medical and public health professionals who evaluate laboratory practices and policies to improve the quality of molecular genetic laboratory services. (cdc.gov)
  • This report also is intended to be a resource for users of laboratory services to aid in their use of molecular genetic tests and test results in health assessment and care. (cdc.gov)
  • Since that time, advances in scientific research and technology have led to a substantial increase both in the health conditions for which genetic defects or variations can be detected with molecular methods and in the spectrum of the molecular testing methods ( 1 ). (cdc.gov)
  • As the number of molecular genetic tests performed for patient testing has steadily increased, so has the number of laboratories that perform molecular genetic testing for heritable diseases and conditions ( 2,3 ). (cdc.gov)
  • With increasing use in clinical and public health practices, molecular genetic testing affects persons and their families in every life stage by contributing to disease diagnosis, prediction of future disease risk, optimization of treatment, prevention of adverse drug response, and health assessment and management. (cdc.gov)
  • By comparing simulation and experimental results, we validated our models and obtained insights. (lu.se)
  • In support of this theory, the agent responsible for the TSE of cattle, called bovine spongiform encephalopathy (BSE), the accepted cause of variant Creutzfeldt-Jakob disease (vCJD) in humans ( 4 ), has been shown to be transmissible to at least 7 species ( 1 ), resulting in propagation of PrP d that retains the characteristic molecular signature of the original BSE prion strain ( 5 - 7 ). (cdc.gov)
  • After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
  • Molecular models help students investigate differences between molecular adhesion, cohesion and capillary actions and enable students to demonstrate surface tension, evaporation, condensation and solubility. (flinnsci.com)
  • However, because of the experimental difficulty in measuring the membrane properties for each leaflet separately, the differences are not well understood at a molecular level. (aip.org)
  • In collaboration with experimental groups, we address these questions on the molecular, cellular, and organ levels with applications in personalized medicine and therapy. (mpi-cbg.de)
  • not unique for the embryonic system but are shared by other ogenesis regulation must consider different scales of multi-cellular modeling areas. (lu.se)
  • Relating in vitro to in vivo exposures with physiologically based tissue dosimetry and tissue response models. (cdc.gov)
  • The P450 3A4 model resembles P450 BM-3 the most, but the B' helix is similar to that of P450eryF, which leads to an enlarged active site when compared with P450 BM-3, P450cam, and P450terp. (nih.gov)
  • Current thinking favors a seeded polymerization model for the conversion of PrP C into PrP d , which has led to the development of several cell-free in vitro conversion model systems ( 8 ). (cdc.gov)
  • The results from docking of progesterone and erythromycin into the enzyme model make it possible to pinpoint residues which may be important for 3A4 function and to target them for site-directed mutagenesis. (nih.gov)
  • The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled. (wikipedia.org)
  • The coordinates of the model were then calculated using a consensus strategy, and the final structure was optimized in the presence of water. (nih.gov)
  • The discovery of the structure of DNA by Francis Crick and James Watson in the early 1950s ushered in a new era in molecular biologic science. (medscape.com)
  • We found that compared to the outer leaflet model, the inner leaflet model had a very bulky and soft structure in the lateral direction. (aip.org)
  • Molecular modeling is the technique to determine the overall structure of an unknown molecule, be it a small one or a macromolecule. (bvsalud.org)
  • Molecular aspects of monooxygenases and bioactivation of toxic compounds. (cdc.gov)
  • Advantages and drawbacks are presented for the different modeling techniques. (aspetjournals.org)
  • Molecular Modeling Techniques and In-Silico Drug Discovery. (bvsalud.org)
  • In this chapter, an overview of the protocol associated with molecular modeling techniques will be discussed. (bvsalud.org)
  • With the development of plastic or polystyrene balls it is now easy to create such models. (wikipedia.org)
  • A reasonable model is based on colon cancer development. (medscape.com)
  • Although the exact process has not been elucidated, the sum of these mutations is believed to lead to cancer development in this model. (medscape.com)
  • The Committee agreed that, despite the considerable progress that had been made in investigating variola virus, significant components of this research, most notably the refinement and use of an animal model developed in 2001 and the development of antiviral drugs, were unlikely to be completed by the end of 2002. (who.int)
  • Learn about DCEG absolute risk models for breast cancer, colon cancer, and melanoma. (cancer.gov)
  • Presenter Stephane Redon, NANO-D Stephane Redon is the former head of the NANO-D research group at the INRIA Grenoble - Rhone-Alpes Research Center, that he started in January 2008 and led until October 2018, when he left to start OneAngstrom, a spin-off of Inria that commercializes the SAMSON open platform for molecular modeling. (foresight.org)
  • Further, during extensive discussion about the potential availability of an animal model, additional research was identified that would necessitate access to live variola virus stocks after the expected 2002 destruction date. (who.int)
  • This is a dynamic process since the crystal structures are improving with time and, therefore, the answers to the models are also changing accordingly. (aspetjournals.org)
  • The calculated electron density profiles along the bilayer normal for each model bilayer system captured well the asymmetric feature of the experimental electron density profile across actual cell plasma membranes, indicating that our procedure of modeling the outer and inner leaflets of the cell plasma membranes was satisfactory. (aip.org)
  • Build large-scale models the whole class can see: this versatile system is perfect for front-of-class demonstrations and lectures. (cochranes.co.uk)
  • DCEG investigators in the Biostatistics Branch have developed models (such as the Gail model) for projecting the individualized absolute risk of certain types of cancer. (cancer.gov)
  • Molecular modelling analysis of the antioxidant activity of probucol. (scialert.net)
  • Molecular modelling analysis of the metabolism of maraviroc. (scialert.net)
  • The construction of physical models is often a creative act, and many bespoke examples have been carefully created in the workshops of science departments. (wikipedia.org)
  • Molecular models help students investigate adhesion, cohesion and capillary actions. (flinnsci.com)