Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Legislation, Drug: Laws concerned with manufacturing, dispensing, and marketing of drugs.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.Drug Industry: That segment of commercial enterprise devoted to the design, development, and manufacture of chemical products for use in the diagnosis and treatment of disease, disability, or other dysfunction, or to improve function.Drug Approval: Process that is gone through in order for a drug to receive approval by a government regulatory agency. This includes any required pre-clinical or clinical testing, review, submission, and evaluation of the applications and test results, and post-marketing surveillance of the drug.Molecular Structure: The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.United StatesUnited States Food and Drug Administration: An agency of the PUBLIC HEALTH SERVICE concerned with the overall planning, promoting, and administering of programs pertaining to maintaining standards of quality of foods, drugs, therapeutic devices, etc.Molecular Sequence Data: 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.Amino Acid Sequence: 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.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).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Molecular Conformation: The characteristic three-dimensional shape of a molecule.Structure-Activity Relationship: 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.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.PaintingsNitrohydroxyiodophenylacetate: Also called 4-hydroxy-3-iodo-5-nitrophenylacetate. A haptenic determinant that can be radiolabeled and used as salts and derivatives for investigations of immunogenic specificity studies.PaintPsilocybine: The major of two hallucinogenic components of Teonanacatl, the sacred mushroom of Mexico, the other component being psilocin. (From Merck Index, 11th ed)Alexander Disease: Rare leukoencephalopathy with infantile-onset accumulation of Rosenthal fibers in the subpial, periventricular, and subependymal zones of the brain. Rosenthal fibers are GLIAL FIBRILLARY ACIDIC PROTEIN aggregates found in ASTROCYTES. Juvenile- and adult-onset types show progressive atrophy of the lower brainstem instead. De novo mutations in the GFAP gene are associated with the disease with propensity for paternal inheritance.ArtSculptureChromosome Painting: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Fatty Acids, Unsaturated: FATTY ACIDS in which the carbon chain contains one or more double or triple carbon-carbon bonds.Linoleic Acid: A doubly unsaturated fatty acid, occurring widely in plant glycosides. It is an essential fatty acid in mammalian nutrition and is used in the biosynthesis of prostaglandins and cell membranes. (From Stedman, 26th ed)Linoleic Acids: Eighteen-carbon essential fatty acids that contain two double bonds.Fatty Acid Desaturases: A family of enzymes that catalyze the stereoselective, regioselective, or chemoselective syn-dehydrogenation reactions. They function by a mechanism that is linked directly to reduction of molecular OXYGEN.Carbon: A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.Desmosterol: An intermediate in the synthesis of cholesterol.Carbon-Carbon Double Bond Isomerases: Enzymes that catalyze the shifting of a carbon-carbon double bond from one position to another within the same molecule. EC 5.3.3.Fatty Acids, Omega-3: A group of fatty acids, often of marine origin, which have the first unsaturated bond in the third position from the omega carbon. These fatty acids are believed to reduce serum triglycerides, prevent insulin resistance, improve lipid profile, prolong bleeding times, reduce platelet counts, and decrease platelet adhesiveness.Carduus: A plant genus of the family ASTERACEAE. Members contain arctiin and onopordopicrin.Glutamine: A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. It is synthesized from GLUTAMIC ACID and AMMONIA. It is the principal carrier of NITROGEN in the body and is an important energy source for many cells.Photography: Method of making images on a sensitized surface by exposure to light or other radiant energy.Glutamate-Ammonia Ligase: An enzyme that catalyzes the conversion of ATP, L-glutamate, and NH3 to ADP, orthophosphate, and L-glutamine. It also acts more slowly on 4-methylene-L-glutamate. (From Enzyme Nomenclature, 1992) EC 6.3.1.2.Animal Fins: Membranous appendage of fish and other aquatic organisms used for locomotion or balance.Light: That portion of the electromagnetic spectrum in the visible, ultraviolet, and infrared range.Baths: The immersion or washing of the body or any of its parts in water or other medium for cleansing or medical treatment. It includes bathing for personal hygiene as well as for medical purposes with the addition of therapeutic agents, such as alkalines, antiseptics, oil, etc.Investments: Use for articles on the investing of funds for income or profit.Sunburn: An injury to the skin causing erythema, tenderness, and sometimes blistering and resulting from excessive exposure to the sun. The reaction is produced by the ultraviolet radiation in sunlight.

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 model

Molecular design software Molecular graphics Molecular modelling Ribbon diagram Software for molecular mechanics modeling Space ... The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction ... Molecular graphics has replaced some functions of physical molecular models, but physical kits continue to be very popular and ... Molecular models have inspired molecular graphics, initially in textbooks and research articles and more recently on computers ...

*Molecular modelling

... nanostructures modeling Molecular design software Molecular engineering Molecular graphics Molecular model Molecular modeling ... Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. ... The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include ... or explicitly modelling electrons of each atom (a quantum chemistry approach). Molecular mechanics is one aspect of molecular ...

*Molecular models of DNA

Molecular modeling of RNA polymerase. Molecular modeling of a bacterial DNA primase template. Molecular modeling of DNA ... Molecular modeling of DNA repair Animated skeletal model of A-DNA. Simplified models of chromatin. Simplified model of ... The DNA model shown (far right) is a space-filling, or CPK, model of the DNA double helix. Animated molecular models, such as ... DNA spacefilling molecular model A model of a designed DNA tetrahedron. 15 m long DNA model, Naturalis Biodiversity Center ...

*Molecular Modelling Toolkit

... which performs common tasks in molecular modelling. The Molecular Modeling Toolkit is a library that implements common ... Konrad Hinsen, The Molecular Modeling Toolkit: A New Approach to Molecular Simulations, As of 28 April 2011[update], MMTK ... "The Molecular Modeling Toolkit: A New Approach to Molecular Simulations". J. Comp. Chem. 21 (2): 79-85. doi:10.1002/(SICI)1096- ... The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, ...

*Molecular Modeling Database

The Molecular Modeling Database (MMDB) is a database of experimentally determined three-dimensional biomolecular structures and ...

*Monte Carlo molecular modeling

... physics List of software for Monte Carlo molecular modeling Software for molecular mechanics modeling Bond fluctuation model ... Monte Carlo molecular modeling is the application of Monte Carlo methods to molecular problems. These problems can also be ... modeled by the molecular dynamics method. The difference is that this approach relies on equilibrium statistical mechanics ... An additional advantage is that some systems, such as the Ising model, lack a dynamical description and are only defined by an ...

*Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA ... Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics) are ... 2008). "GPU acceleration of cutoff pair potentials for molecular modeling applications". In CF'08: Proceedings of the 2008 ... "Accelerating molecular modeling applications with graphics processors". Journal of Computational Chemistry. 28 (16): 2618-2640 ...

*List of software for Monte Carlo molecular modeling

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 ... Dubbeldam, David; Calero, Sofía; Ellis, Donald E.; Snurr, Randall Q. (26 February 2015). "RASPA: molecular simulation software ... Scienomics Chameleon classical molecular and coarse grain Spartan classical Tinker classical (download is free of charge) Zori ...

*Comparison of software for molecular mechanics modeling

... molecular modeling List of software for nanostructures modeling Molecular design software Molecular dynamics Molecular modeling ... CS1 maint: Uses authors parameter (link) Macke T, Case DA (1998). "Modeling unusual nucleic acid structures". Molecular ... Resources Short list of Molecular Modeling resources OpenScience Biological Magnetic Resonance Data Bank Materials modelling ... Modeling of Nucleic Acids: 379-393. A. Górecki; M. Szypowski; M. Długosz; J. Trylska (2009). "RedMD - Reduced molecular ...

*Hartree-Fock method

Hinchliffe, Alan (2000). Modelling Molecular Structures (2nd ed.). Baffins Lane, Chichester, West Sussex PO19 1UD, England: ... In the Bohr model of the atom, the energy of a state with principal quantum number n is given in atomic units as E = − 1 / n 2 ... The full molecular wave function is actually a function of the coordinates of each of the nuclei, in addition to those of the ... In molecular calculations a similar approach is sometimes used by first calculating the wave function for a positive ion and ...

*Molecular mechanics

Molecular modeling on GPU Comparison of software for molecular mechanics modeling List of software for Monte Carlo molecular ... Molecular mechanics uses classical mechanics to model molecular systems. The Born-Oppenheimer approximation is assumed valid ... Computational Chemistry and Molecular Modeling: Principles and Applications. Berlin: Springer. ISBN 3-540-77302-9. Molecular ... Boas FE, Harbury PB (July 2008). "Design of Protein-Ligand Binding Based on the Molecular-Mechanics Energy Model". J Mol Biol. ...

*Energy minimization

"Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures". J. Chem. Inf. Model. 56 (10): 1963-1978. ... The computational model that provides an approximate E(r) could be based on quantum mechanics (using either density functional ... Using this computational model and an initial guess (or ansatz) of the correct geometry, an iterative optimization procedure is ... The computational model of chemical bonding might, for example, be quantum mechanics. As an example, when optimizing the ...

*Outline of natural science

History of molecular mechanics - history of the uses Newtonian mechanics to model molecular systems. History of Flavor ... Molecular mechanics - uses Newtonian mechanics to model molecular systems. Flavor chemistry - someone who uses chemistry to ... branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules ... history of the branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological ...

*CPK coloring

Ball-and-stick model Molecular graphics Software for molecular modeling Robert B. Corey and Linus Pauling (1953): Molecular ... The scheme is named after the CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter ... doi:10.1063/1.1770803 Walter L. Koltun (1965), Space filling atomic units and connectors for molecular models. U. S. Patent ... the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. ...

*Q-Chem

ISBN 978-0-471-33368-5. Quantum Computational Software; Molecular Modeling; Visualization Banned By Gaussian A.I. Krylov, P.M.W ... methods for excited states Janus QM/MM interface YinYang Atom model without linked atoms ONIOM model EFP method (including ... Q-Chem 4.0 comes with the new graphical interface, IQMol which includes hierarchical input generator, molecular builder, and ... Computational Molecular Science. R.J. Bartlett (2012). "Coupled-cluster theory and its equation-of-motion extensions". Wiley ...

*Anna Krylov

"Quantum Computational Software; Molecular Modeling; Visualization". www.Q-Chem.com. Retrieved 2 January 2018. ... 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 ... Size-consistent wave functions for bond-breaking: The equation-of-motion spin-flip model Chem. Phys. Lett., 338, 375-384 (2001 ...

*Møller-Plesset perturbation theory

ISBN 0-9636769-4-6. Leach, Andrew R. (1996). Molecular Modelling. Harlow: Longman. pp. 83-85. ISBN 0-582-23933-8. Levine, Ira N ... 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" (abstract). ...

*Austin Model 1

"Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model ... Austin Model 1, or AM1, is a semi-empirical method for the quantum calculation of molecular electronic structure in ... Leach, Andrew R. (2001). Molecular Modelling. Pearson Education Limited. ISBN 0-582-38210-6. ... the first of a new series of general purpose quantum mechanical molecular models". Tetrahedron. 49 (23): 5003. doi:10.1016/ ...

*Darunavir

Molecular Modeling. 20: 2122. doi:10.1007/s00894-014-2122-y. CS1 maint: Explicit use of et al. (link) McKeage, K; Perry, CM; ... Model. 52: 1542-1558. doi:10.1021/ci300014z. CS1 maint: Explicit use of et al. (link) King, N. M.; Prabu-Jeyabalan, M.; et al ... "WHO Model List of Essential Medicines (19th List)" (PDF). World Health Organization. April 2015. Archived (PDF) from the ... binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular ...

*Outline of chemistry

History of molecular mechanics - history of the uses Newtonian mechanics to model molecular systems. History of Flavor ... Molecular mechanics - applies classical mechanics to model molecular systems. Nanotechnology - study and application of matter ... The John Dalton Model J. J. Thomson: The Plum Pudding Model Thermochemistry Thermochemistry - Chemical kinetics - is the study ... Molecular biology - study of interactions between the various systems of a cell. It overlaps with biochemistry. ...

*X-PLOR

... and computational molecular biology. Comparison of software for molecular mechanics modeling Molecular mechanics Güntert, Peter ...

*Extensible Computational Chemistry Environment

Support for building molecular models. Graphical user interface to a broad range of electronic structure theory types. ... Molecular orbitals and vibrational frequencies are among the properties displayed. Support for importing results from NWChem, ... Three-dimensional visualization and graphical display of molecular data properties while jobs are running and after completion ...

*Outline of physical science

History of molecular mechanics - history of the uses Newtonian mechanics to model molecular systems. History of Flavor ... Molecular structure Quantum chemistry Spectroscopy Theoretical chemistry Electron configuration Molecular modelling Molecular ... Kinetic molecular theory Phases of matter and phase transitions Temperature and thermometers Energy and heat Heat flow: ... History of mechanochemistry - history of the coupling of the mechanical and the chemical phenomena on a molecular scale and ...

*Olfactory receptor

Their sequences exhibit typical class A GPCR motifs, useful for building their structures with molecular modeling. Golebiowski ... Journal of Molecular Modeling. 13 (3): 401-9. doi:10.1007/s00894-006-0160-9. PMID 17120078. Smith, RS; Peterlin, Z; Araneda, RC ... Using mathematical modeling and computer simulations, Tian et al proposed an evolutionarily optimized three-layer regulation ... Buck L, Axel R (April 1991). "A novel multigene family may encode odorant receptors: a molecular basis for odor recognition". ...

*Low-frequency collective motion in proteins and DNA

Journal of Molecular Modeling. 15: 1545. doi:10.1007/s00894-009-0577-z. Chou KC (Dec 1983). "Identification of low-frequency ... The quasi-continuum model is one model developed to identify and analyze this kind of low-frequency motions in protein and DNA ... This model operates on an intermediate level of complexity between the elastic global model, which treats the biomolecule as a ... Chou KC, Maggiora GM, Mao B (Aug 1989). "Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA ...

*Phage display

Endemann H, Model P (July 1995). "Location of filamentous phage minor coat proteins in phage and in infected cells". J. Mol. ... This technology was further developed and improved by groups at the Laboratory of Molecular Biology with Greg Winter and John ... Initial work was done by laboratories at the MRC Laboratory of Molecular Biology (Greg Winter and John McCafferty), the Scripps ...
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 ...
Structure prediction of small (up to 150 amino acids) globular proteins has improved so much that it has become nearly as accurate as low resolution experimental methods [1]. However, there is still a serious bottleneck in membrane protein structure prediction. The number of membrane protein structures deposited in Protein Data Bank (PDB) is much smaller than that for globular proteins. As a consequence, PDB provides relatively weak statistics for membrane proteins. There are two families of membrane proteins which still lack adequate characterization though they represent important drug targets. The first family is a well-known family of G protein-coupled receptors (GPCRs) which share a common structural motif of seven transmembrane helices. The second one is less known and more structurally diverse family of solute carrier transporters (SLCs).. For many years G protein-coupled receptors have been drug targets for many diseases including neurological, cardiovascular, endocrinological disorders. ...
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
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... , Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
... , 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 ...
Todays energy functions are not able yet to distinguish reliably between correct and almost correct protein models. Improving these near-native models is currently a major bottle-neck in homology modeling or experimental structure determination at low resolution. Increasingly accurate energy functions are required to complete the "last mile of the protein folding problem," for example during a molecular dynamics simulation. We present a new approach to reach this goal. For 50 high resolution X-ray structures, the complete unit cell was reconstructed, including disordered water molecules, counter ions, and hydrogen atoms. Simulations were then run at the pH at which the crystal was solved, while force-field parameters were iteratively adjusted so that the damage done to the structures was minimal. Starting with initial parameters from the AMBER force field, the optimization procedure converged at a new force field called YAMBER (Yet Another Model Building and Energy Refinement force field), ...
Using a fragment-based docking procedure, several small-molecule inhibitors of caspase-3 were identified and tested and the crystal structures of three inhibitor complexes were determined. The crystal structures revealed that one inhibitor (NSC 18508) occupies only the S1 subsite, while two other inhibitors (NSC 89167 and NSC 251810) bind only to the prime part of the substrate-binding site. One of the major conformational changes observed in all three caspase-3-inhibitor complexes is a rotation of the Tyr204 side chain, which blocks the S2 subsite. In addition, the structural variability of the residues shaping the S1-S4 as well as the S1 subsites supports an induced-fit mechanism for the binding of the inhibitors in the active site. The high-resolution crystal structures reported here provide novel insights into the architecture of the substrate-binding site, which might be useful for the design of more potent caspase inhibitors. ...
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 ...
Main Page of the Computational Chemistry Group. Scientific interests: Free Energy calculations, QM/MM method, PAW-method, Biological Nitrogen Fixation by Nitrogenase, sodium nitroprusside
... 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 ...
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)], ...
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. ...
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 ...
Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discovery of HDAC8 inhibitors, we developed two pharmacophore models containing six and five pharmacophoric features, respectively, using the representative structures from two molecular dynamic (MD) simulations performed in Gromacs 4.0.5 package. Various analyses of trajectories obtained from MD simulations have displayed the changes upon inhibitor binding. Thus utilization of the dynamically-responded protein structures in pharmacophore development has the added advantage of considering the conformational flexibility of protein. The MD trajectories were clustered based on single-linkage method and representative
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. ...
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 ...
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
Extended Hückel theory and the method of perturbative configuration interaction using localized orbitals (PCILO) predict strikingly different results for the conformation of histamine cations. Extend Hückel theory predicts that both mono- and dications should exist as mixtures of trans and gauche forms, as observed with NMR studies in solution, whereas PCILO predicts a strong preference of the monocation for the gauche form and of the dication for the trans form, as shown by X-ray crystallography. In order to resolve this dilemma, nonempirical ab initio computations have been performed for the two species. They confirm the results of the PCILO calculations and indicate that the intrinsic conformational preferences of the isolated molecule correspond closely to the crystal structure data. In order to elucidate the situation prevailing in solution, the principal hydration sites of the histamine cations have been determined by calculations ab initio, and new conformational energy maps have been ...
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The ClH⋯FH and FH⋯ClH configurations of the mixed HF/HCl dimer (where the donor⋯acceptor notation indicates the directionality of the hydrogen bond) as well as the transition state connecting the two configurations have been optimized using MP2 and CCSD(T) with correlation consistent basis sets as large as aug-cc-pV(5 + d)Z. Harmonic vibrational frequencies confirmed that both configurations correspond to minima and that the transition state has exactly one imaginary frequency. In addition, anharmonic vibrational frequencies computed with second-order vibrational perturbation theory (VPT2) are within 6 cm-1 of the available experimental values and deviate by no more than 4 cm-1 for the complexation induced HF frequency shifts ...
A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue α/β protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.. ...
The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-GlyNMe (1) has been carried out by using a combination of theoretical calculations and experimental (H-1 and C-13 NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,-trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N-or C-terminal amide group in cis-conformation, are observed separately and located 13.0 +/- 2 kJmol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJmol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is ...
Binary patterning (the arrangement of hydrophobic and polar amino acids) and electrostatics are important determinants of the stability and conformational specificity of designed proteins. We have developed methods to to select the optimal binary pattern and model electrostatics in protein design studies. The Genclass method of binary patterning uses a solvent accessible surface generated from backbone coordinates of the target fold and "generic" side chains, constructs whose size and shape are similar to an average amino acid. Each position is classified according to the solvent exposure of its generic side chain. The method was tested by analyzing several proteins in the Protein Data Bank and by experimentally characterizing homeodomain variants whose binary patterns were systematically varied. Selection of the optimal binary pattern results in a designed protein that is monomeric, well-folded, and hyperthermophilic. Homeodomain variants with fewer hydrophobic residues are destabilized, ...
This picture of the determinants of anion-cation selectivity for the CNG channels differs from that currently envisaged for the cation selectivity of K+ channels. In KcsA, the appropriate electrostatic environment for cations within the pore is considered to be predominantly (∼80%) the result of pore helix dipoles projected toward the internal cavity at the interior end of the selectivity filter (Roux and MacKinnon, 1999; Roux et al., 2000). In contrast for CNG channels, we suggest that pore helix dipoles are not critical for determining anion-cation selectivity but, as indicated above, that this is determined by the polarity of the 0′ residues. However, as discussed earlier, we do suggest that these pore helix dipoles may contribute to the outward rectification of the E0′K/R mutant CNG channels in symmetrical solutions.. It should also be noted that a recent study on the role of the pore helix dipoles in the inward rectifier (Kir2.1), in which positive charges were introduced in the K+ ...
1NC8: High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
1NC8: High-resolution solution NMR structure of the minimal active domain of the human immunodeficiency virus type-2 nucleocapsid protein.
Protein Structures via Force Field X (FFX) Protein structures are now provided on gene pages where available. These structures were modeled using Force Field X, an atomic resolution molecular modeling application. A promising source of evidence for classifying genetic variants is atomic resolution physics-based simulation techniques, which can test physical hypotheses about pathogenic mechanisms more rapidly and at a lower cost than many experimental approaches (e.g. model organisms). However, protein structural models (e.g. from X-ray crystallography, NMR, or homology modeling) required for simulation of hearing-related proteins are often based on imperfect experimental information (e.g. low-resolution diffraction) or may contain defects due to limited homology. We combine an advanced polarizable potential energy function, novel many-body optimization theory, and GPU-acceleration to locally and globally optimize all available deafness-associated protein models through the Force Field X (FFX) ...
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Several novel techniques are employed for protein tertiary structure prediction, but the more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures. However, a critical look at the yearly
As we have seen a flipping out movement in the N-terminal region (Fig. 3a), we investigated the N-terminal end (residues Arg 2-Gln 7) showing high fluctuations in the RMSF plot (Fig. 2b) for local fluctuations and conformational transitions. From the T-pad analysis (Fig. 5) it can be proposed that the short transition at Val 3, transition at the two glutamines at positions 4 and 7 and fluctuation at Lys 6 are responsible for the flipping out nature as evidenced by the high PAD degrees in the range of 61°-74° (Fig. 7). The possible mechanism for closed conformation of the N-terminal loop at pH 7 is that it was maintained via a series of hydrophobic interactions between the N-terminal loop and the loop connecting β3 and H2 (L3,2). Here, the L3,2 contains both polar and non-polar amino acids which are not stimulated by their protonation state; hence the aliphatic side chains of L1,2 form a series of hydrophobic interactions (Additional file 5). In case of the free energy representative structure ...
TY - JOUR. T1 - Structural insights into steroid hormone binding. AU - Valjakka, Jarkko. AU - Takkinen, Kristiina. AU - Teerinen, Tuija. AU - Söderlund, Hans. AU - Rouvinen, Juha. PY - 2002. Y1 - 2002. N2 - The monoclonal anti-testosterone antibody (3-C4F5) has a relatively high affinity (3 × 108 M −1) with an overall good specificity profile. However, the earlier characterized binding properties have shown that both the affinity and specificity of this antibody must be improved if it is intended for use in clinical immunoassays. In this paper, the crystal structures of the recombinant anti-testosterone (3-C4F5) Fab fragment have been determined in the testosterone-bound and free form at resolutions of 2.60 and 2.72 Å, respectively. The high affinity binding of the (3-C4F5) Fab is mainly determined by shape complementarity between the protein and testosterone. Only one direct hydrogen bond is formed between the hydroxyl group of the testosterone D-ring and the main-chain oxygen of Gly100JH. ...
Background: Techniques for inferring the functions of the protein by comparing their shape similarity have been receiving a lot of attention. Proteins are functional units and their shape flexibility occupies an essential role in various biological processes. Several shape descriptors have demonstrated the capability of protein shape comparison by treating them as rigid bodies. But this may give rise to an incorrect comparison of flexible protein shapes. Results: We introduce an efficient approach for comparing flexible protein shapes by adapting a local diameter (LD) descriptor. The LD descriptor, developed recently to handle skeleton based shape deformations [1], is adapted in this work to capture the invariant properties of shape deformations caused by the motion of the protein backbone. Every sampled point on the protein surface is assigned a value measuring the diameter of the 3D shape in the neighborhood of that point. The LD descriptor is built in the form of a one dimensional histogram ...
Link for Professor Gonzalez. Abstract: Over the past two decades, stunning breakthroughs in the field of structural biology have continued to produce groundbreaking high-resolution structures of large, multi-component biomolecular machines. Comparative analyses of these static structures reveals the remarkable conformational flexibility of these machines and hints at the significant structural rearrangements that evidently accompany their functional cycles. Unfortunately, the experimental observation and characterization of these conformational dynamics is severely impeded by the size and complexity of biomolecular machines, severely limiting our understanding of the contributions that dynamics make to their functions. Using a combination of molecular genetic-, biochemical-, and single-molecule biophysical approaches, my research group aims to overcome these challenges and elucidate the precise roles that the conformational dynamics of biomolecular machines play in driving and controlling their ...
In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting
The conformation-independent structural comparison tool ProSMART (Procrustes Structural Matching Alignment and Restraints Tool) is designed to allow fast but detailed comparative analysis of macromolecular structures in the presence of conformational changes. ProSMART is suited to the analysis of the structural conservation of local backbone and side chains in a wide variety of scenarios: the method is sensitive enough to allow identification of subtle dissimilarities between structures sharing high sequence homology, whilst being versatile enough to scale to the identification of surprising local similarities between more distantly related structures.. ProSMART compares local structures using n-residue backbone fragments. These constructs allow comparisons to be performed at a chosen level of structural resolution or at multiple resolutions (note that this does not refer to crystallographic resolution, but rather to the level of structural detail). In contrast with most other features (e.g. ...
Motivation:In silico methods are being widely used for identifying substrates for various kinases and deciphering cell signaling networks. However, most of the available phosphorylation site prediction methods use motifs or profiles derived from a known data set of kinase substrates and hence, their applicability is limited to only those kinase families for which experimental substrate data is available. This prompted us to develop a novel multi-scale structure-based approach which does not require training using experimental substrate data.. Results:In this work, for the first time, we have used residue-based statistical pair potentials for scoring the binding energy of various substrate peptides in complex with kinases. Extensive benchmarking on Phospho.ELM data set indicate that our method outperforms other structure-based methods and has a prediction accuracy comparable to available sequence-based methods. We also demonstrate that the rank of the true substrate can be further improved, if ...
David Sherrill, a leader in the field of computational studies of stacking interactions, from the Georgia Institute of Technology in Atlanta, US, says: What this paper seems to show is that in some cases pi-pi interactions can be enhanced by breaking the aromaticity to yield localised pi orbitals. This is a big surprise, and I think most of the community would not have expected that result, he says. It is commonly the case that when one is making some supramolecular systems, the presence of an aromatic interaction is considered the favourable recognition element, and it still is. But now, I think we can broaden our view to look at a wider variety of these recognition elements, he adds ...
Knowledge of a protein three dimensional structure facilitates understanding of molecular mechanisms that underlie processes essential for living organisms, such as metabolic and signaling pathways, and immunological responses. It can also be used to control these functionalities through drugs designed in silico. Experimental determination of 3D structures is expensive, time consuming and, in some cases, not yet possible. For example, most membrane protein structures are unknown due to the specific environment of cell membranes, their typically large size and dynamic behavior. If homologous structures are available, computer modeling can be an alternative to experimental techniques. In some cases, partial structural information is available, such as residue-residue contact sites, which can also be applied to full protein reconstruction. If there is no structural data on any similar protein, threading and de novo methods can be applied to obtain coarse approximations of the target. Over 80 and ...
one of commercially important fish species in China. Then, 3-D structure model of the mullet IL-22 was constructed by comparative modeling method using human IL-22 (1M4R) as template, and a 5 ns molecular dynamics (MD) was studied. The open reading frame (ORF) of mullet IL-22 cDNA was 555 bp, encoding 184 amino acids. The mullet IL-22 shared higher identities with the other fish IL-22 homologs and possessed a conserved IL-10 signature motif at its C-terminal. The mullet IL-22 model possessed six conserved helix structure. PROCHECK, SAVES and Molprobity server analysis confirmed that this model threaded well with human IL-22. Strikingly, analysis with CastP, cons-PPISP server suggested that the cysteines in mullet IL-22 might not be involved in the forming of disulfide bond for structural stabilization, but related to protein-protein interactions ...
It is nice that the prediction performance can be improved a lot if applied to more realistic NMR-derived ensembles. This is expected because the experimental chemical shift of a given nucleus reflects the Boltzmann-weighted average of the instantaneous chemical shifts of a large number of conformational substates that interconvert on the millisecond timescale or faster. This behavior has been discussed many times in the literature. All Ubiquitin NMR structures cited in this work are generated specifically to be a more realistic presentation of protein ensemble in solutions, except 1D3Z. 1D3Z is a traditional NMR structure model, where NMR conformer "bundle" should not be confused with a dynamic ensemble representation of the protein. In these types of NMR models, the spread of atomic positions merely provides information about the uncertainties of the atomic positions with respect to the average structure and has no direct physical meaning. The author may need to provide more comments on this ...
It is nice that the prediction performance can be improved a lot if applied to more realistic NMR-derived ensembles. This is expected because the experimental chemical shift of a given nucleus reflects the Boltzmann-weighted average of the instantaneous chemical shifts of a large number of conformational substates that interconvert on the millisecond timescale or faster. This behavior has been discussed many times in the literature. All Ubiquitin NMR structures cited in this work are generated specifically to be a more realistic presentation of protein ensemble in solutions, except 1D3Z. 1D3Z is a traditional NMR structure model, where NMR conformer "bundle" should not be confused with a dynamic ensemble representation of the protein. In these types of NMR models, the spread of atomic positions merely provides information about the uncertainties of the atomic positions with respect to the average structure and has no direct physical meaning. The author may need to provide more comments on this ...
It is nice that the prediction performance can be improved a lot if applied to more realistic NMR-derived ensembles. This is expected because the experimental chemical shift of a given nucleus reflects the Boltzmann-weighted average of the instantaneous chemical shifts of a large number of conformational substates that interconvert on the millisecond timescale or faster. This behavior has been discussed many times in the literature. All Ubiquitin NMR structures cited in this work are generated specifically to be a more realistic presentation of protein ensemble in solutions, except 1D3Z. 1D3Z is a traditional NMR structure model, where NMR conformer "bundle" should not be confused with a dynamic ensemble representation of the protein. In these types of NMR models, the spread of atomic positions merely provides information about the uncertainties of the atomic positions with respect to the average structure and has no direct physical meaning. The author may need to provide more comments on this ...
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Synonyms for a-helix in Free Thesaurus. Antonyms for a-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for a-helix?
Abstract. The prediction of binding modes (BMs) occurring between a small molecule and a target protein of biological interest has become of great importance for drug development. The overwhelming diversity of needs leaves room for docking approaches addressing specific problems. A Fast docking using the CHARMM force field with EADock DSS for the Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design of drug-like molecules by a fragment-based molecular evolutionary approach. HIV-1 P24-derived peptides were examined to predict anti-HIV-1 activity among them. The efficacy of the prediction has already been validated in vitro. Our in silico experimental studies performed on the mentioned peptides, which may lead to new anti-HIV-1 peptide-mimotopic therapeutics candidates. In this research study we presented for the first time a computational approach and a combined molecular docking-based and pharmacophore-based target prediction strategy ...
Hi Andrew: andrew holway wrote: , Multi reference quantum chem. Gaussian and Molcas. Without doing a benchmark it will be quite hard to indicate which one may be faster. Barcelona is a quad core with a good memory system (relative to the Clovertown). If your problems are large enough to spill to disk for matrix elements, then it isnt likely that the CPU performance would be the dominating factor. If you have enough ram that your problem remains in ram (as I remember, multi-reference qchem tends to be ... large ...) then you may find that your performance is more dominated by memory access patterns, for which Barcelona might be better. If you were doing pure DFT, well, that can, for some problems, fit almost entirely in cache. In which case, it makes sense to get the largest cache chip you can get. As usual, real use case tests are the most realistic predictor of performance. Joe , Andy -- Joseph Landman, Ph.D Founder and CEO Scalable Informatics LLC, email: landman at scalableinformatics.com ...
The importance of electrostatic interactions in soft matter and biological systems can often be traced to non-uniform charge effects, which are commonly described using a multipole expansion of the corresponding charge distribution. The standard approach when extracting the charge distribution of a given system is to treat the constituent charges as points. This can, however, lead to an overestimation of multipole moments of high order, such as dipole, quadrupole, and higher moments. Focusing on distributions of charges located on a spherical surface - characteristic of numerous biological macromolecules, such as globular proteins and viral capsids, as well as of inverse patchy colloids - we develop a novel way of representing spherical surface charge distributions based on the von Mises-Fisher distribution ...
I spent a couple days at the Schrödinger User Symposium in Portland recently. I was really impressed with the topics presented at the conference. I was humbled at how little I know about computational chemistry, but I appreciate the geniuses working in drug discovery. For example, one speaker (Michael Podvinec) shared about the development of drugs to treat a viral infection called Dengue Fever. This disease affects 50 million people and kills 12,000 per year . The people working on a cure or vaccine for this and other deadly diseases analyze complex 3D molecules to determine whether compounds can perform a needed function. Although I dont understand More… 3D , stereoscopic , molecular modeling , Schrödinger , computational chemistry ...
With the Classroom Molecular Model Set, students build molecular models. Color-coded atom centers are designed to accept bonds at the proper angle so students will gain understanding of the three-dimensional character of molecules.
The light chain CDR1 (LCDR1) loop of FI6v3 makes two contacts with the side of helix A, opposite the side that contributes to the hydrophobic groove; Phe27D makes hydrophobic contact with the aliphatic part of Lys39, and Asn28 hydrogen bonds to Asn43, together accounting for a buried surface area of about 190 Å2 for both H1 and H3. With H1 HA, which was cocrystallized in the uncleaved form, LCDR1 also makes extensive contact with the uncleaved "fusion peptide" of the neighboring HA monomer (Fig. 3, B and C, and Fig. 4, A and B), which accounts for an additional 320 Å2 of FI6v3 buried surface. Residues 28 and 29 of LCDR1 make main-chain amide hydrogen bonds with the main-chain carbonyls of HA1 residue 329 and the next-but-one residue, Leu2, of HA2 and thus span the cleavage site. Phe27D of LCDR1 makes hydrophobic contacts with Leu2 of the neighboring HA2, whereas the side-chain hydroxyl of Tyr29 hydrogen bonds to the main-chain carbonyl of residue 325 of the neighboring HA1 chain. In contrast ...
An apparatus and method for treating obesity and for delivering time-released medicaments is described and which includes a plurality of space-filling portions which are sized to be received within a human patients body and which come together in a patients body to form a structure which provides therapeutic benefit to the patient. In the method of the present invention, the method includes providing a plurality of space-filling portions which are sized to be received within the patients body; and inserting the space-filling portions into the body of the patient and wherein the respective space-filling portions come together following insertion into the body to form a structure providing therapeutic benefit to the patient.
The usual conference conversation starts with "Hey X, how are things going?", "Oh, fine, and you?", "Oh, fine." But one person responded "Writing a lot of proposals and getting them rejected." I really appreciated this honesty, and it makes me feel less bad about my own rejections. A few weeks ago I had a similar talk with another colleagues about the possibility of having no PhD students in the not-too-distant future and how this affects the choice of research projects one can take on. I think a lot of scientists are going through the same type of thing and it is important to be open about it ...
title: A system for collecting and curating sightseeing information toward satisfactory tour plan creation abstract: Satisfactory tour planning entails providing tourists with tour plans that reflect both static information, such as tourists preferences and profiles; and dynamic information, such as crowded sightseeing spots and congested paths to these spots. Collecting, maintaining, and curating such dynamic information imposes a lot of time, monetary, and labor costs on those who manage tourist spots and the tourists themselves. In this paper, we propose a system that uses two novel mechanisms: (1) a participatory collection mechanism that efficiently and timely collects and updates both static and dynamic information about tourist spots and paths; and (2) a content curation mechanism that selects important items from the collected information and compiles them into tour plans. We conducted a pilot study where two categories of people, those who make plans before sightseeing and those who do ...
CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here ...
CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here ...
The peptide bond has considerable double-bond character and this prevents rotation around that bond in the polypeptide chain. Adjacent amino acids can adopt different configurations by rotation around the two other bonds in the backbone. The angle of the bond between the nitrogen atom (blue) and the α-carbon atom (black) is Φ (phi) and the angle of the bond between the α-carbon atom and the carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]. These angles are measured in degrees where 180° is the angle of the bonds when all of the atoms of both residues lie in the most extended conformation. Rotation in one direction is positive so the values go from 0° to 180° and in the other direction they go from 0° to -180°. (180° = -180° in this notation ...
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Franz Joseph Gall 1758-1828 was he could predict a buy Reviews ins house by autoantibody-producing mice on their use. In 1796 he contributed a role of the many land. This microfluidic buy signed hemorrhagic in the Such manner, well in the USA.
... presents experimental or theoretical research results of outstanding significance and timeliness on asymmetry in organic,...
L-leucine 4-methoxy-beta-naphthylamide hydrochloride;4467-68-9;H-leu-4m-betana hcl;H-leu-4mbna hcl;L-leu-4-methoxy-beta-naphthylamide hcl;L-leucine 4-methoxy-beta-naphthylamide hydrochloride;L-leucyl-4-methoxy-beta-naphthylamide hydrochloride;TS77403.Tetrahedron
Dispersion-corrected DFT, such as B3LYP-D3, are not new functionals but a mix of conventional functionals and an add-on energy term. For example, B3LYP-D3 denotes a calculation with the usual B3LYP functional plus a D3 dispersion correction energy term. The dispersion correction energy term is a relatively simply function of interatomic distances and contain adjustable parameters that are fitted to conformational and interaction energies computed using CCSD(T)/CBS. The fitting is done for a given functional. DFT-D and DFT-D2 energy corrections consider all pairs of atoms while DFT-D3 also consider triplets of atoms to account for three-body effects ...
Enzymes are nanomachines that are exceptionally efficient at catalyzing a chemical reaction. They play a role in all cellular mechanisms. Like all proteins, they are made up of amino acid chains that are folded and assembled in a very precise 3D structure. Some enzymes, like ribonuclease A, are so efficient that they catalyze the transformation of chemical molecules thousands of times per second.. In this study, Donald Gagné, a researcher in Professor Doucets lab holding a PhD in biology from INRS, analyzed the impact of removing a methyl group located near a loop distant from the reaction site of ribonuclease A-a very slight change that presumably would have no effect. The mutation does not perturb the 3D structure of the enzyme. However, it did result in a four-fold reduction in the affinity of ribonuclease A for nucleotides (molecules to which it must bind to carry out its function). How is this possible?. Using crystallography techniques and nuclear magnetic resonance to examine the enzyme ...
Residues present on the surface of the proteins are involved in a number of functions, especially in ligand-protein interactions, that are important for drug design. The residues present in the core of the protein provide stability to the protein and help in maintaining protein structure. Hence, there is a need for a binary characterization of protein residues based on their surface accessibility (surface accessible or buried). Such a classification can aid in the directed study of either residue type. A number of methods for the prediction of surface accessible protein residues have been proposed in the past. However, most of these methods are computationally complex and time consuming. In this thesis, we propose a simple method based on protein sequence homology parameters for the binary classification of protein residues as surface accessible or "buried". To aid in the classification of protein residues, we chose three highly conservative homology-based parameter filter thresholds. The filter ...
A technique for identifying folding patterns of proteins using mass spectrometry that is potentially faster and requires less sample than X-ray crystallographic or NMR methods has been developed by B.W. Gibson and I.D. Kuntz. They believe the time needed to determine the fold family of a protein can be reduced to one week and that less than 10mg of protein may be required to elucidate macromolecular interactions, and multiple conformational states, and to contribute to the design of protein mimetics ...
My docking experiments of OSM-S-106 vs all crystal structures of Plasmodium kinases supports PKA (protein kinase A) as the top target (PDB 5kbf).. OSM-S-106 was docked into the ligand binding site with the target side chains free to rotate as described in the previous entry. The docked structure was then energy minimized in Yasara with the Yasara2 force field with explicit water molecules in a 6A dodecahedral box. Three cycles of simulated annealing energy minimization were performed. The energy minimized coordinates are attached. Visual inspection showed that OSM-S-106 was bound quite tightly in its pocket, especially the sulfonamide end, leaving little room for chemical extension. This would be consistent with the SAR data.. All the compounds in Series 3 were then aligned to the cAMP site using a combined ligand-based and force-field based method in Cresset Forge, with protein structure (pdb 5kbf) set as medium strength restraints. I then created a number of modifications of OSM-S-106 that I ...
Profacgen, a US-based biotech company, has added one additional molecular modeling service, protein structure modeling, to its existing custom protein services.. The three-dimensional structure of a protein provides essential information about its biological function and facilitates the design of therapeutic drugs that specifically bind to the protein target. Recent years have witnessed a tremendous increase in the number of experimentally determined protein structures. It is, however, still generally tedious and time-consuming to solve protein structures with experimental approaches. Therefore, computational approaches represent an alternative and supplement to experimental methods to obtain three-dimensional structure of a protein.. By taking advantages of computational modeling methods, Profacgen is able to predict the three-dimensional structure of proteins of its customers interest. Over the years, Profacgen has accumulated abundant experience with the modeling of various kinds of ...
The current status of docking procedures for predicting protein-protein interactions starting from their three-dimensional (3D) structure is reassessed by evaluating blind predictions, performed during 2003-2004 as part of Rounds 3-5 of the community-wide experiment on Critical Assessment of PRedicted Interactions (CAPRI). Ten newly determined structures of protein-protein complexes were used as targets for these rounds. They comprised 2 enzyme-inhibitor complexes, 2 antigen-antibody complexes, 2 complexes involved in cellular signaling, 2 homo-oligomers, and a complex between 2 components of the bacterial cellulosome. For most targets, the predictors were given the experimental structures of 1 unbound and 1 bound component, with the latter in a random orientation. For some, the structure of the free component was derived from that of a related protein, requiring the use of homology modeling. In some of the targets, significant differences in conformation were displayed between the bound and ...
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The mechanisms by which JAK2 is activated by the prevalent pseudokinase (JH2) V617F mutation in blood cancers remain elusive. Via structure-guided mutagenesis and transcriptional and functional assays, we identify a community of residues from the JH2 helix αC, SH2-JH2 linker and JH1 kinase domain that mediate V617F-induced activation. This circuit is broken by altering the charge of residues along the solvent-exposed face of the JH2 αC, which is predicted to interact with the SH2-JH2 linker and JH1. Mutations that remove negative charges or add positive charges, such as E596A/R, do not alter the JH2 V617F fold, as shown by the crystal structure of JH2 V617F E596A. Instead, they prevent kinase domain activation via modulation of the C-terminal residues of the SH2-JH2 linker. These results suggest strategies for selective V617F JAK2 inhibition, with preservation of wild type function. ...
Molecular dynamics (MD) simulation is a technique that aids in the understanding of fundamental processes in biology and chemistry, and has important technological applications in pharmacy, biotechnology, and nanotechnology. Many complex molecular processes have cascades of timescales spanning the range from 10-15 s to 1 s, often with no pronounced gap that would permit efficient coarse-grained time integration.. In many applications, the slowest timescales and the associated structural rearrangements are the ones of interest. In this project, we study the challenging process of induced folding of peptides. Such states may be found when peptide ligands bind to proteins and when membrane-associated proteins anchor into the membrane. Here, association and conformational changes occur on physical timescales of nano- to milliseconds, while dissociation events may require seconds or longer.. The long-term aims of this project are to develop efficient modeling and simulation methods for the dominant ...
Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most experiments of the unfolding process have been fit to two-state and/or one dimensional models, with the details of the protein and its dynamics often subsumed into a zero-force unfolding rate and a distance x(u)(1D) to the transition state. We consider the entire phase space of a model protein under a constant force, and show that x(u)(1D) contains a sizeable contribution from exploring the full multidimensional energy landscape. This effect is greater for proteins with many degrees of freedom that are affected by force; and surprisingly, we predict that externally attached flexible linkers also contribute to the measured unfolding characteristics. ...
Given some similarity in sequence between two proteins, a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. This approach, which is often...
Protein folding prediction is a non-convex optimization problem very relevant in biology. It consists in predicting the three dimensional structure of a protein molecule starting from the sequence information alone. The complexity of this problem arises from many sources: in the first place the search space is huge because an astonishing number of different conformations have to be considered in order to find the currect one. In second place evaluating each model is hard since thousands of atomic interactions have to be computed during and the energy description currently available is only an approximation of the true energy. Many large scale projects have been established to develop PSP tools and to perform predictions of real protein structures using both supercomputers and distributed computing , nevertheless the key to achieve reliable predictions is yet to be found. Simplified representation models such as the HP model (bottom right) preserve a considerable complexity (HP-PSP is NP-hard) ...
multihelical; 3-helical bundle similar to one half of the DEATH domain fold is flanked by two alpha-hairpins forming a four-helical bundle; the axes of the three-helical and four-helical bundles are aproximately orthogonal to each other ...
Bcl-xL is a member of the Bcl-2 family of apoptotic regulators, responsible for inhibiting the permeabilization of the mitochondrial outer membrane, and a promising anti-cancer target. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (a) a soluble folded conformation, (b) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (c) refolded membrane-inserted conformations, for which no structural data are available. Previous studies established that in the cell Bcl-xL exists in a dynamic equilibrium between soluble and membranous states, however, no direct evidence exists in support of either anchored or inserted conformation of the membranous state in vivo. In this in vitro study, we employed a combination of fluorescence and EPR spectroscopy to characterize structural features of the bilayer-inserted conformation of Bcl-xL and the lipid modulation of its membrane insertion transition. Our ...

Contacts: Karen McNulty Walsh, (631) 344-8350 or Peter Genzer, (631) 344-3174printerPrint

Scientists Reveal Details of Calcium Safety-Valve in Cells

Structure of membrane protein that plays a role in signaling cell death could be new target for anticancer drugs

June 6, 2014

A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive ...
New, license-free DNA ladders will allow researchers to estimate the size of fragments of DNA for a fraction of the cost of currently available methods.
We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a major drug target family. The method is a combination of the ligand- and target-based pharmacophore methods and founded on the extraction of structural fragments, interacting ligand moiety and receptor residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We describe how the library fragments are recombined and inferred to build pharmacophores for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element ...
Ten lowest-energy conformers (best 20%) from the plainQ calculation. Depictions are as in Figure 6, but the Ca2+ ions are also shown, as gray spheres. The non-c
Substrate cleavage by metalloproteinases involves nucleophilic attack on the scissile peptide bond by a water molecule that is polarized by a catalytic metal, usually a zinc ion, and a general base, usually the carboxyl group of a glutamic acid side chain
XlaeOBP peptides corresponding to putative epitopes thought to be localized outside the OBP hydrophobic binding pocket and exhibiting the right calculated antigenicity were chosen as sequences C64Qâ  Y79. They were synthesized, both conjugated to ...
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.
TY - JOUR. T1 - Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis. T2 - The case of histone lysine methyltransferase SET7/9. AU - Wang, Shenglong. AU - Hu, Po. AU - Zhang, Yingkai. PY - 2007/4/12. Y1 - 2007/4/12. N2 - To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean ...
Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Iron atom in PDB 2mgl: High Resolution Crystal Structures Of Five Distal Histidine Mutants of Sperm Whale Myoglobin
A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair. In this manner, two nucleobases, one on each strand, can be held together by hydrogen bonds in the major groove. A Hoogsteen base pair applies the N7 position of the purine base (as a hydrogen bond acceptor) and C6 amino group (as a donor), which bind the Watson-Crick (N3-N4) face of the pyrimidine base. Ten years after James Watson and Francis Crick published their model of the DNA double helix, Karst Hoogsteen reported a crystal structure of a complex in which analogues of A and T formed a base pair that had a different geometry from that described by Watson and Crick. Similarly, an alternative base-pairing geometry can occur for G•C pairs. Hoogsteen pointed out that if the alternative hydrogen-bonding patterns were present in DNA, then the double helix would have to assume a quite different shape. Hoogsteen base pairs are, however, rarely observed. Hoogsteen pairs have quite different properties ...
TY - JOUR. T1 - Binding interface of cardiac potassium channel proteins identified by hydrogen deuterium exchange of synthetic peptides. AU - Chen, Jerri. AU - Angeletti, Ruth. AU - McDonald, Thomas V.. AU - Xiao, Hui. PY - 2012/5. Y1 - 2012/5. N2 - Three synthetic peptides, derived from the human potassium channel proteins Ether-a-go-go-related gene (HERG), KCNQ1, and KCNE1, were investigated by hydrogen deuterium exchange coupled with electrontransfer dissociation mass spectrometry at single residue resolution. Each amino acid residue in the first half of the HERG peptide incorporated deuterons with a higher rate than those in the second half of the peptide, consistent with the nuclear magnetic resonance structure of this peptide, with amino acids 1-10 being a flexible coil, whereas amino acids 11-24 are a stable amphipathic helix. The binding interface of KCNQ1 and KCNE1 was determined by comparing the difference of sequential fragment ions before and after binding. The residues determined to ...
In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible.. ...
The method for distribution function computation of the spherical particles size is evaluated on the model curves. This method is based on the direct integral transformation of the entire small angle X-ray scattering indicatrix. The efficiency of the method is confirmed, its resistance to the statistical noise is tested and the distortion caused by the limitation of the experimental scattering curve is estimated. Experimental curves of small angle scattering are obtained for the composite materials formed by nanosized diamond particles in pyrocarbon matrix. The distribution function of nanoparticles size is calculated by means of this method. The correlation between the distribution function and the thickness of the pyrocarbon layer is found.

Inspiration: Vintage Molecular Models | Apartment TherapyInspiration: Vintage Molecular Models | Apartment Therapy

... but we cant help loving the look of these vintage molecular models ... but we cant help loving the look of these vintage molecular models. We first spotted them at our friend Jeremys pad when we ...
more infohttps://www.apartmenttherapy.com/inspiration-vintage-molecular-88643

Molecular Models by Maggie Hathcoat on PreziMolecular Models by Maggie Hathcoat on Prezi

Transcript of Molecular Models. Molecular Models. enzymes. sugars. dehydration synthesis. hydrolysis. peptide bond. glycosidic ...
more infohttps://prezi.com/r85ljj2vpwx3/molecular-models/

Molecular Modeling | BSC-CNSMolecular Modeling | BSC-CNS

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. ...
more infohttps://www.bsc.es/research-and-development/research-areas/molecular-modeling

Molecular Modeling | BSC-CNSMolecular Modeling | BSC-CNS

Molecular recognition is the basis of biological function. Docking is among a number of structural bioinformatics strategies ... As one of our main research lines, we model enzymatic activity addressing not only the atomic (and electronic) detailed ... of computational methodology for the structural and energetic characterization of protein interactions at molecular level. ... trying to understand molecular recognition, both to understand structure to function relationships in macromolecules, and to ...
more infohttps://www.bsc.es/es/research-and-development/research-areas/molecular-modeling

Molecular modeling - Bioinformatics.Org WikiMolecular modeling - Bioinformatics.Org Wiki

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 ...
more infohttp://bioinformatics.org/wiki/Molecular_modelling

Molecular modeling and simulation | Open LibraryMolecular modeling and simulation | Open Library

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 = ...
more infohttps://openlibrary.org/works/OL16282642W/Molecular_modeling_and_simulation

Orbit Molecular Models Kit | Carolina.comOrbit Molecular Models Kit | Carolina.com

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 ...
more infohttps://www.carolina.com/cochranes-molecular-models/orbit-molecular-models-kit/840222.pr

Molecular Modeling of Chemoreceptor:Ligand Interactions | SpringerLinkMolecular Modeling of Chemoreceptor:Ligand Interactions | SpringerLink

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. ...
more infohttps://link.springer.com/protocol/10.1007/978-1-4939-7577-8_28

BB2280 Molecular Modeling 7.5 credits | KTHBB2280 Molecular Modeling 7.5 credits | KTH

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 ...
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MolyMod molecular models sets | Sigma-AldrichMolyMod molecular models sets | Sigma-Aldrich

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 ...
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Molecular modeling of antigenic peptideMolecular modeling of antigenic peptide

... S. Ramakrishnan ramakris at podunk.cps.msu.edu Wed May 26 14:10:50 EST 1993 *Previous ... I am interested in molecular modeling of Antigenic peptide of M Leprae and its interaction with T cell CD4+ with the MHCII ... Is the structure of MHCII known with the coordinates so that this input can be used to model and study the interaction between ...
more infohttp://www.bio.net/bionet/mm/immuno/1993-May/000371.html

new links in molecular modelingnew links in molecular modeling

... arthur roberts arthurr at WSUNIX.WSU.EDU Mon Jun 14 11:03:46 EST 1999 *Previous message: ... biophysicist and molecular biologist. This site is constantly evolving and expanding, so it can be easy to use, reliable, and ...
more infohttp://www.bio.net/bionet/mm/molmodel/1999-June/001458.html

Computational Chemistry and Molecular Modeling Support GroupComputational Chemistry and Molecular Modeling Support Group

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Computational Chemistry & Molecular Modeling | Chemistry | Subjects | WileyComputational Chemistry & Molecular Modeling | Chemistry | Subjects | Wiley

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?. ...
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Molecular modeling of glycosyltransferases.  - PubMed - NCBIMolecular modeling of glycosyltransferases. - PubMed - NCBI

Molecular modeling of glycosyltransferases.. Imberty A1, Wimmerová M, Koca J, Breton C. ... Nevertheless, only a limited number of crystal structures is available and molecular modeling appears to be an inescapable tool ... Because of sequence diversity and limited experimental data, molecular modeling of these enzymes is not straightforward and ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/17072009?dopt=Abstract

MOAC MSc Module CH926 - Molecular ModellingMOAC MSc Module CH926 - Molecular Modelling

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; ...
more infohttps://warwick.ac.uk/fac/sci/moac/degrees/moac/ch926/

Foundations of Molecular Modeling and Simulation | SpringerLinkFoundations of Molecular Modeling and Simulation | SpringerLink

Density Functional Theory FOMMS 2015 Molecular Dynamics Molecular Simulation Molecular modeling Monte Carlo Simulation ... molecular science, and engineering simulation. The theme of the 2015 meeting focuses on Molecular Modeling and the Materials ... Optimizing Molecular Models Through Force-Field Parameterization via the Efficient Combination of Modular Program Packages ... Atomistic Modeling and Simulation for Solving Gas Extraction Problems Genri E. Norman, Vasily V. Pisarev, Grigory S. Smirnov, ...
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How to build molecular modelsHow to build molecular models

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Molecular Model | Technology TrendsMolecular Model | Technology Trends

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Molecular model kitMolecular model kit

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Molecular model kits | Periodic table shopMolecular model kits | Periodic table shop

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INTERNET SOURCES FOR MOLECULAR MODELINGINTERNET SOURCES FOR MOLECULAR MODELING

a. NIH Guide to Molecular Modeling. b. docking tutorial. c. organic chemistry resources. d. molecular modeling. e. molecular ... A GUIDE TO INTERNET SOURCES FOR MOLECULAR MODELING. The Internet has an incredible variety of resources that could be useful to ... Click on A guide to some useful internet resources for - THE GENERAL COURSE and then in the Molecular Modeling Section, select ... Click on Scientific Resources, then Molecular Modeling Home Page.Click on Knowledge and Onramp to get an unbelievable amount of ...
more infohttp://employees.csbsju.edu/hjakubowski/classes/ch331public/molmd1.html

Translation Molecular Model Kit | Carolina.comTranslation Molecular Model Kit | Carolina.com

Kit contains enough parts to create a 15-nucleotide model of mRNA (including a stop codon) and 4 tRNAs with their specific ... Translation Molecular Model Kit. Item # 211116 *bvseo_sdk, java_sdk, bvseo-4.0.0 ... Kit contains enough parts to create a 15-nucleotide model of mRNA (including a stop codon) and 4 tRNAs with their specific ... Kit contains enough parts to create a 15-nucleotide model of mRNA (including a stop codon) and 4 tRNAs with their specific ...
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Molecular modeling of the chromatosome particle.  - PubMed - NCBIMolecular modeling of the chromatosome particle. - PubMed - NCBI

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 ...
more infohttps://www.ncbi.nlm.nih.gov/pubmed/12853645
  • Models encompass a wide range of degrees of precision and engineering: some models such as J.D. Bernal's water are conceptual, while the macromodels of Pauling and Crick and Watson were created with much greater precision. (wikipedia.org)
  • 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)
  • 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)
  • The "sticks" used in the model to represent single covalent bonds were not the shortest available in this molecular modelling kit and may more commonly be used to model double or triple bonds but have been selected in this case to make it is easier for viewers to appreciate approximate angles from photographs of the model. (buzzine.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)
  • Because of sequence diversity and limited experimental data, molecular modeling of these enzymes is not straightforward and utilizes the most recent tools, such as fold recognition programs. (nih.gov)
  • I am interested in molecular modeling of Antigenic peptide of M Leprae and its interaction with T cell CD4+ with the MHCII complex .I have chosen an antigenic peptide of 12k obtained from field trials in India.Is there any other proven antigenic peptide of m-lepray?If so what is the amino acid sequence? (bio.net)
  • 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)
  • 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)
  • Molecular models are as vital a tool for the study of chemistry as calculators are for the study of mathematics. (buzzine.com)
  • Nevertheless, only a limited number of crystal structures is available and molecular modeling appears to be an inescapable tool for rationalization of binding data, engineering of enzyme properties, and design of inhibitors that would be of interest as therapeutic compounds. (nih.gov)
  • After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
  • A total of 20 university credits (hp) in Biotechnology or Molecular Biology. (kth.se)
  • The importance of stereochemistry was not then recognised and the model is essentially topological (it should be a 3-dimensional tetrahedron). (wikipedia.org)
  • B ) Model of the gH1d (cartoon representation) complexed with DNA (ribbon). (nih.gov)
  • The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. (wikipedia.org)