Journal ArticleDOI
Dynamics of folded proteins
TLDR
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.Abstract:
The dynamics of a folded globular protein (bovine pancreatic trypsin inhibitor) have been studied by solving the equations of motion for the atoms with an empirical potential energy function. The results provide the magnitude, correlations and decay of fluctuations about the average structure. These suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.read more
Citations
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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
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.
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Gromacs 4.5
Sander Pronk,Szilárd Páll,Szilárd Páll,Roland Schulz,Roland Schulz,Per Larsson,Pär Bjelkmar,Pär Bjelkmar,Rossen Apostolov,Rossen Apostolov,Michael R. Shirts,Jeremy C. Smith,Jeremy C. Smith,Peter M. Kasson,David van der Spoel,David van der Spoel,Berk Hess,Berk Hess,Erik Lindahl,Erik Lindahl,Erik Lindahl +20 more
TL;DR: A range of new simulation algorithms and features developed during the past 4 years are presented, leading up to the GROMACS 4.5 software package, which provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
Book ChapterDOI
Interaction Models for Water in Relation to Protein Hydration
TL;DR: In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.
References
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Journal ArticleDOI
Correlations in the Motion of Atoms in Liquid Argon
TL;DR: In this article, a system of 864 particles interacting with a Lennard-Jones potential and obeying classical equations of motion has been studied on a digital computer (CDC 3600) to simulate molecular dynamics in liquid argon at 94.4 degrees K and a density of 1.374 g.
Journal ArticleDOI
Dynamics of ligand binding to myoglobin
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Journal ArticleDOI
Exposure of tryptophanyl residues in proteins. Quantitative determination by fluorescence quenching studies.
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Related Papers (5)
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