Molecular mechanical potential functions and their application to study molecular systems
Identifieur interne : 004916 ( Main/Exploration ); précédent : 004915; suivant : 004917Molecular mechanical potential functions and their application to study molecular systems
Auteurs : Wendy D. Cornell [États-Unis] ; Allison E. Howard [États-Unis] ; Peter Kollman [États-Unis]Source :
- Current Opinion in Structural Biology [ 0959-440X ] ; 1991.
English descriptors
- Teeft :
- Alanyl dipeptide, Aliphatic amines, Amber force field, Amino acids, Annealing, Aromatic molecules, Atomic charges, Atomic dipoles, Atomic point charges, Benzene, Best agreement, Best correlation, Biol, Biomol struct, Biopolymers, Bond lengths, Bond rotations, Carbonyl groups, Carlo, Cartesian derivatives, Charge flux, Charge transfer, Charmm, Charmm force field, Chem, Chem phys, Comp chem, Comput, Comput cbem, Comput chem, Computational time, Computationally, Conformation, Conformational, Conformational analysis, Conformational sampling, Constant dielectric, Constraint, Coulombic interaction, Crambin, Crystal structure, Crystalline hydrates, Crystallographic data, Crystallographic structure, Cutoff, Derivative, Dielectric, Diffraction data, Dihedral space, Dinur, Dynamics, Ecepp potentials, Electron density, Electronegativity, Electronegativity gradient, Electronegativity parameters, Electrostatic force, Electrostatic interactions, Empirical force fields, Energy conservation, Energy functions, Energy hypersurface, Energy refinement, Energy surface, Equilibrium geometry, Experimental data, Force constants, Force field, Force field calculations, Force fields, Fourier series, Free energy, Functional form, Functional forms, Good agreement, Higher correlations, Higher multipoles, Initial geometry, Initio, Initio calculations, Initio energy surfaces, Initio quantum mechanics, Initio values, Intermolecular terms, Internal coordinates, Ionic molecules, Kollman, Lattice, Lattice constants, Lattice energies, Liquid benzene, Liquid properties, Liquid water, Local minima, Lone pairs, Lowenergy conformations, Many groups, Mndo, Mndo wave functions, Model systems, Modeling metalloproteins, Molecular dynamics, Molecular dynamics simulations, Molecular mechanics, Molecule, Monopole model, Monte carlo methods, Monte carlo simulations, More time, Nuclear distance constraints, Nucleic acids, Orbital electronegativity method, Organic molecule, Pairwise interactions, Parameter, Partial charges, Partial equalization, Peptide, Periodic boundary conditions, Phys, Phys chem, Planar dimers, Point dipoles, Polarizability, Polypeptide, Potential energy, Potential energy surface, Potential functions, Potential functions cornell, Protein crambin, Protein structure, Protein tendamistat, Quality structure, Quantum mechanics, Radial distribution function, Reaction rates, Refinement, Relative bond asymmetry, Second derivatives, Second moments, Second peak, Simpler representations, Simulating protein, Simulation, Small model systems, Small molecules, Solution conformation, Solvated protein, Solvation, Solvent effects, Spectroscopic force fields, Structural biology, Structural data, Structural transitions, Structure factors, Such methods, Technical issues, Theoryand simulation, Thermal motion, Thermodynamic properties, Torsion, Torsional, Torsional parameters, Total interaction energy, Transition state, Various approaches, Vibrational frequencies, Waals parameters, Water model, Water models, Wave function, Weiner.
Abstract
Abstract: In this review, we attempt to describe the critical issues involved in the parameterization and use of molecular mechanical force fields. This review contains six sections: an introduction to the issues; a description of the technical issues in molecular mechanics; comparisons and evaluations of force fields; improving and extending force fields; combining force fields with experimental data; and conformational searching.
Url:
DOI: 10.1016/0959-440X(91)90062-X
Affiliations:
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<term>Aliphatic amines</term>
<term>Amber force field</term>
<term>Amino acids</term>
<term>Annealing</term>
<term>Aromatic molecules</term>
<term>Atomic charges</term>
<term>Atomic dipoles</term>
<term>Atomic point charges</term>
<term>Benzene</term>
<term>Best agreement</term>
<term>Best correlation</term>
<term>Biol</term>
<term>Biomol struct</term>
<term>Biopolymers</term>
<term>Bond lengths</term>
<term>Bond rotations</term>
<term>Carbonyl groups</term>
<term>Carlo</term>
<term>Cartesian derivatives</term>
<term>Charge flux</term>
<term>Charge transfer</term>
<term>Charmm</term>
<term>Charmm force field</term>
<term>Chem</term>
<term>Chem phys</term>
<term>Comp chem</term>
<term>Comput</term>
<term>Comput cbem</term>
<term>Comput chem</term>
<term>Computational time</term>
<term>Computationally</term>
<term>Conformation</term>
<term>Conformational</term>
<term>Conformational analysis</term>
<term>Conformational sampling</term>
<term>Constant dielectric</term>
<term>Constraint</term>
<term>Coulombic interaction</term>
<term>Crambin</term>
<term>Crystal structure</term>
<term>Crystalline hydrates</term>
<term>Crystallographic data</term>
<term>Crystallographic structure</term>
<term>Cutoff</term>
<term>Derivative</term>
<term>Dielectric</term>
<term>Diffraction data</term>
<term>Dihedral space</term>
<term>Dinur</term>
<term>Dynamics</term>
<term>Ecepp potentials</term>
<term>Electron density</term>
<term>Electronegativity</term>
<term>Electronegativity gradient</term>
<term>Electronegativity parameters</term>
<term>Electrostatic force</term>
<term>Electrostatic interactions</term>
<term>Empirical force fields</term>
<term>Energy conservation</term>
<term>Energy functions</term>
<term>Energy hypersurface</term>
<term>Energy refinement</term>
<term>Energy surface</term>
<term>Equilibrium geometry</term>
<term>Experimental data</term>
<term>Force constants</term>
<term>Force field</term>
<term>Force field calculations</term>
<term>Force fields</term>
<term>Fourier series</term>
<term>Free energy</term>
<term>Functional form</term>
<term>Functional forms</term>
<term>Good agreement</term>
<term>Higher correlations</term>
<term>Higher multipoles</term>
<term>Initial geometry</term>
<term>Initio</term>
<term>Initio calculations</term>
<term>Initio energy surfaces</term>
<term>Initio quantum mechanics</term>
<term>Initio values</term>
<term>Intermolecular terms</term>
<term>Internal coordinates</term>
<term>Ionic molecules</term>
<term>Kollman</term>
<term>Lattice</term>
<term>Lattice constants</term>
<term>Lattice energies</term>
<term>Liquid benzene</term>
<term>Liquid properties</term>
<term>Liquid water</term>
<term>Local minima</term>
<term>Lone pairs</term>
<term>Lowenergy conformations</term>
<term>Many groups</term>
<term>Mndo</term>
<term>Mndo wave functions</term>
<term>Model systems</term>
<term>Modeling metalloproteins</term>
<term>Molecular dynamics</term>
<term>Molecular dynamics simulations</term>
<term>Molecular mechanics</term>
<term>Molecule</term>
<term>Monopole model</term>
<term>Monte carlo methods</term>
<term>Monte carlo simulations</term>
<term>More time</term>
<term>Nuclear distance constraints</term>
<term>Nucleic acids</term>
<term>Orbital electronegativity method</term>
<term>Organic molecule</term>
<term>Pairwise interactions</term>
<term>Parameter</term>
<term>Partial charges</term>
<term>Partial equalization</term>
<term>Peptide</term>
<term>Periodic boundary conditions</term>
<term>Phys</term>
<term>Phys chem</term>
<term>Planar dimers</term>
<term>Point dipoles</term>
<term>Polarizability</term>
<term>Polypeptide</term>
<term>Potential energy</term>
<term>Potential energy surface</term>
<term>Potential functions</term>
<term>Potential functions cornell</term>
<term>Protein crambin</term>
<term>Protein structure</term>
<term>Protein tendamistat</term>
<term>Quality structure</term>
<term>Quantum mechanics</term>
<term>Radial distribution function</term>
<term>Reaction rates</term>
<term>Refinement</term>
<term>Relative bond asymmetry</term>
<term>Second derivatives</term>
<term>Second moments</term>
<term>Second peak</term>
<term>Simpler representations</term>
<term>Simulating protein</term>
<term>Simulation</term>
<term>Small model systems</term>
<term>Small molecules</term>
<term>Solution conformation</term>
<term>Solvated protein</term>
<term>Solvation</term>
<term>Solvent effects</term>
<term>Spectroscopic force fields</term>
<term>Structural biology</term>
<term>Structural data</term>
<term>Structural transitions</term>
<term>Structure factors</term>
<term>Such methods</term>
<term>Technical issues</term>
<term>Theoryand simulation</term>
<term>Thermal motion</term>
<term>Thermodynamic properties</term>
<term>Torsion</term>
<term>Torsional</term>
<term>Torsional parameters</term>
<term>Total interaction energy</term>
<term>Transition state</term>
<term>Various approaches</term>
<term>Vibrational frequencies</term>
<term>Waals parameters</term>
<term>Water model</term>
<term>Water models</term>
<term>Wave function</term>
<term>Weiner</term>
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<front><div type="abstract" xml:lang="en">Abstract: In this review, we attempt to describe the critical issues involved in the parameterization and use of molecular mechanical force fields. This review contains six sections: an introduction to the issues; a description of the technical issues in molecular mechanics; comparisons and evaluations of force fields; improving and extending force fields; combining force fields with experimental data; and conformational searching.</div>
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<name sortKey="Howard, Allison E" sort="Howard, Allison E" uniqKey="Howard A" first="Allison E." last="Howard">Allison E. Howard</name>
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