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Biological Responses to Engineered Nanomaterials: Needs for the Next Decade.Recent advances in QM/MM free energy calculations using reference potentialsLarge-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysisPath Similarity Analysis: A Method for Quantifying Macromolecular PathwaysUnbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of TrajectoriesGeneralized Ensemble Sampling of Enzyme Reaction Free Energy PathwaysMultiscale enhanced sampling of intrinsically disordered protein conformations.Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.A simple molecular mechanics integrator in mixed rigid body and dihedral angle space.Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulationsFree-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.Enhancing protein adsorption simulations by using accelerated molecular dynamics.Enhanced ligand sampling for relative protein-ligand binding free energy calculationsStructural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase.Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL.MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methodsMultiscale methods for computational RNA enzymology.Generating reservoir conformations for replica exchange through the use of the conformational space annealing methodPerspective: Quantum mechanical methods in biochemistry and biophysics.Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.Atomistic Monte Carlo simulation of lipid membranes.Collective variable approaches for single molecule flexible fitting and enhanced sampling.Enhanced Monte Carlo Sampling through Replica Exchange with Solute TemperingPerspective: Coarse-grained models for biomolecular systems.Atomistic-level portrayal of drug-DNA Interplay: a history of courtships and meetings revealed by molecular simulations.Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.Molecular dynamics simulations of heterogeneous cell membranes in response to uniaxial membrane stretches at high loading ratesEquilibrium Ensembles for Insulin Folding from Bias-Exchange Metadynamics.Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" modelsSimulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.A single-walker approach for studying quasi-nonergodic systems.Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.Communication: Multiple atomistic force fields in a single enhanced sampling simulation.Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.Systematic Dissociation Pathway Searches Guided by Principal Component Modes.
P2860
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P2860
description
2011 nî lūn-bûn
@nan
2011 թուականին հրատարակուած գիտական յօդուած
@hyw
2011 թվականին հրատարակված գիտական հոդված
@hy
2011年の論文
@ja
2011年論文
@yue
2011年論文
@zh-hant
2011年論文
@zh-hk
2011年論文
@zh-mo
2011年論文
@zh-tw
2011年论文
@wuu
name
Equilibrium sampling in biomolecular simulations
@ast
Equilibrium sampling in biomolecular simulations
@en
Equilibrium sampling in biomolecular simulations
@nl
type
label
Equilibrium sampling in biomolecular simulations
@ast
Equilibrium sampling in biomolecular simulations
@en
Equilibrium sampling in biomolecular simulations
@nl
prefLabel
Equilibrium sampling in biomolecular simulations
@ast
Equilibrium sampling in biomolecular simulations
@en
Equilibrium sampling in biomolecular simulations
@nl
P2860
P921
P3181
P1476
Equilibrium sampling in biomolecular simulations
@en
P2093
Daniel M Zuckerman
P2860
P3181
P356
10.1146/ANNUREV-BIOPHYS-042910-155255
P407
P577
2011-01-01T00:00:00Z