Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.
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Bridging scales through multiscale modeling: a case study on protein kinase AEnzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy PartitionComputing the relative stabilities and the per-residue components in protein conformational changes.A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobinUnassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics.Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE ParallelizationAtomically detailed simulation of the recovery stroke in myosin by MilestoningFree energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials.Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.Studying functional dynamics in bio-molecules using accelerated molecular dynamics.Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitinMultiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.Early events in helix unfolding under external forces: a milestoning analysis.Perspective: Computer simulations of long time dynamicsCoiled-coil response to mechanical force: global stability and local crackingAnalyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.The structural dynamics of macromolecular processes.Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.Exploring energy landscapes: from molecular to mesoscopic systems.Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning.Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses.Computational study of peptide permeation through membrane: Searching for hidden slow variables.Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with MilestoningTransient non-native hydrogen bonds promote activation of a signaling protein.Milestoning without a Reaction CoordinateAn automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis.Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories.Thermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example.Milestoning simulation reveals mechanism of helix-breaking.Steady-state simulations using weighted ensemble path sampling.Experiments and comprehensive simulations of the formation of a helical turnAn adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates.Exact milestoning.Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase.Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
P2860
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P2860
Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.
description
2007 nî lūn-bûn
@nan
2007年の論文
@ja
2007年学术文章
@wuu
2007年学术文章
@zh
2007年学术文章
@zh-cn
2007年学术文章
@zh-hans
2007年学术文章
@zh-my
2007年学术文章
@zh-sg
2007年學術文章
@yue
2007年學術文章
@zh-hant
name
Extending molecular dynamics t ...... inetics in a solvated peptide.
@en
Extending molecular dynamics t ...... inetics in a solvated peptide.
@nl
type
label
Extending molecular dynamics t ...... inetics in a solvated peptide.
@en
Extending molecular dynamics t ...... inetics in a solvated peptide.
@nl
prefLabel
Extending molecular dynamics t ...... inetics in a solvated peptide.
@en
Extending molecular dynamics t ...... inetics in a solvated peptide.
@nl
P2093
P2860
P356
P1476
Extending molecular dynamics t ...... inetics in a solvated peptide.
@en
P2093
Anthony M A West
David Shalloway
P2860
P304
P356
10.1063/1.2716389
P407
P577
2007-04-01T00:00:00Z