Journal ArticleDOI
Molecular dynamics simulations in biology.
Martin Karplus,Gregory A. Petsko +1 more
TLDR
Molecular dynamics is also being used to determine protein structures from NMR, to refine protein X-ray crystal structures faster from poorer starting models, and to calculate the free energy changes resulting from mutations in proteins.Abstract:
Molecular dynamics—the science of simulating the motions of a system of particles—applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. Knowledge of these motions provides insights into biological phenomena such as the role of flexibility in ligand binding and the rapid solvation of the electron transfer state in photosynthesis. Molecular dynamics is also being used to determine protein structures from NMR, to refine protein X-ray crystal structures faster from poorer starting models, and to calculate the free energy changes resulting from mutations in proteins.read more
Citations
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Journal ArticleDOI
All-atom empirical potential for molecular modeling and dynamics studies of proteins.
Alexander D. MacKerell,D. Bashford,M. Bellott,Roland L. Dunbrack,Jeffrey D. Evanseck,Martin J. Field,Stefan Fischer,Jiali Gao,H. Guo,S. Ha,Diane Joseph-McCarthy,L. Kuchnir,K. Kuczera,F. T. K. Lau,C. Mattos,Stephen W. Michnick,Thien H. Ngo,D. T. Nguyen,B. Prodhom,W. E. Reiher,Benoît Roux,M. Schlenkrich,Jeremy C. Smith,Roland H. Stote,John E. Straub,Masakatsu Watanabe,J. Wiórkiewicz-Kuczera,D. Yin,Martin Karplus +28 more
TL;DR: The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals.
Book
X-PLOR Version 3.1: A System for X-ray Crystallography and NMR
TL;DR: This manual to X-PLOR Version 3.1 presents the theoretical background, syntax and function of the programme and also provides a comprehensive list of references and sample input files with comments.
Journal ArticleDOI
Combining evolutionary information and neural networks to predict protein secondary structure.
Burkhard Rost,Chris Sander +1 more
TL;DR: This work extends the previous three‐level system of neural networks by using additional input information derived from multiple alignments using a position‐specific conservation weight as part of the input to increase performance and greatly increased accuracy.
Journal ArticleDOI
Empirical force fields for biological macromolecules: overview and issues.
TL;DR: An overview of the issues associated with the development and application of empirical force fields to biomolecular systems and a summary of the force fields commonly applied to the different classes of biomolecules are presented.
Journal ArticleDOI
Proton transfer in solution: Molecular dynamics with quantum transitions
TL;DR: In this article, the authors apply the surface-hopping method to proton transfer in solution, where the quantum particle is an atom, using full classical mechanical molecular dynamics for the heavy atom degrees of freedom, including the solvent molecules.
References
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Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
Crystallographic R Factor Refinement by Molecular Dynamics
TL;DR: Test cases showed that the need for manual corrections during refinement of macromolecular crystal structures is reduced and the dynamics calculation moved residues that were misplaced by more than 3 angstroms into the correct positions without human intervention.
Journal ArticleDOI
Dynamics of folded proteins
TL;DR: The dynamics of a folded globular protein have been studied by solving the equations of motion for the atoms with an empirical potential energy function and suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.
Journal ArticleDOI
Improved simulation of liquid water by molecular dynamics
TL;DR: In this paper, a four-charge model for each molecule and a modification of the prior ''BNS'' interaction was proposed to improve the fidelity of the molecular dynamics simulation, leading to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x-ray scattering experiments.
Book
Dynamics of proteins and nucleic acids
TL;DR: In this paper, the structure of proteins, nucleic acids, and their solvent surroundings is discussed. And theoretical methods are used to model the dynamics of proteins and nucleic acid interactions.