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
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TLDR
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.Abstract:
New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...read more
Citations
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Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids.
TL;DR: The Kemp elimination reaction of benzisoxazole via piperidine was computed in 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6] using mixed quantum and molecular mechanics (QM/MM) simulations and was found to give close agreement with the experimental free energy of activation.
Journal ArticleDOI
Theoretical and computational models of biological ion channels
TL;DR: The goal of this review is to establish a broad and rigorous theoretical framework to describe ion permeation through biological channels on the basis of the statistical mechanical projection-operator formalism of Mori and Zwanzig.
Journal ArticleDOI
Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules
TL;DR: The AMOEBA force field performs well across different environments and phases, and the key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
Journal ArticleDOI
High-resolution crystal structure of human protease-activated receptor 1
Cheng Zhang,Yoga Srinivasan,Daniel H. Arlow,Juan Jose Fung,Juan Jose Fung,Daniel Palmer,Yaowu Zheng,Yaowu Zheng,Hillary F. Green,Anjali Pandey,Ron O. Dror,David E. Shaw,William I. Weis,Shaun R. Coughlin,Brian K. Kobilka +14 more
TL;DR: The structure of human PAR1 bound to vorapaxar will aid the development of improved PAR1 antagonists and the discovery of antagonists to other members of this receptor family.
Journal ArticleDOI
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.
Michael R. Shirts,Vijay S. Pande +1 more
TL;DR: TIP3P-MOD, a model designed to give improved free energy of hydration for methane, gives uniformly the closest match to experiment; it is found that the ability to accurately model pure water properties does not necessarily predict ability to predict solute/solvent behavior.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
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.