Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
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The evolutionary portrait of metazoan NAD salvageExtending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction spaceComputational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptorsFreeSolv: a database of experimental and calculated hydration free energies, with input filesGMCT : A Monte Carlo simulation package for macromolecular receptorsEnsemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamicsGuidelines for the analysis of free energy calculationsImplicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.Lead optimization mapper: automating free energy calculations for lead optimization.Alchemical prediction of hydration free energies for SAMPL.Perspective: Alchemical free energy calculations for drug discovery.Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.Are current atomistic force fields accurate enough to study proteins in crowded environments?Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field.Potential energy functions for atomic-level simulations of water and organic and biomolecular systemsPredicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.Modeling aqueous solvation with semi-explicit assembly.Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume termsMultipole electrostatics in hydration free energy calculations.Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation.Solvation properties of N-acetyl-β-glucosamine: molecular dynamics study incorporating electrostatic polarization.Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir.Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.Comparison of free energy methods for molecular systems.Application of a polarizable force field to calculations of relative protein-ligand binding affinitiesProtein-directed self-assembly of a fullerene crystal.Determination of partial molar volumes from free energy perturbation theory.The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability.A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence.All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields.Physical Modeling of Aqueous Solvation.Exploring the free-energy landscapes of biological systems with steered molecular dynamics.Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: case study of relative binding free energies of fructose-1,6-bisphosphatase inhibitors.Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations.
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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins
description
article
@en
im September 2003 veröffentlichter wissenschaftlicher Artikel
@de
wetenschappelijk artikel
@nl
наукова стаття, опублікована у вересні 2003
@uk
name
Extremely precise free energy ...... nics force fields for proteins
@en
Extremely precise free energy ...... nics force fields for proteins
@nl
type
label
Extremely precise free energy ...... nics force fields for proteins
@en
Extremely precise free energy ...... nics force fields for proteins
@nl
prefLabel
Extremely precise free energy ...... nics force fields for proteins
@en
Extremely precise free energy ...... nics force fields for proteins
@nl
P2093
P2860
P356
P1476
Extremely precise free energy ...... nics force fields for proteins
@en
P2093
Jed W. Pitera
Vijay S. Pande
William C. Swope
P2860
P304
P356
10.1063/1.1587119
P407
P577
2003-09-15T00:00:00Z