Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece
about
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulationsEverything you wanted to know about Markov State Models but were afraid to askTaming the complexity of protein foldingSimulating oligomerization at experimental concentrations and long timescales: A Markov state model approachPrinciples and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsQwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.The protein folding problemUsing Markov state models to study self-assemblyMarkov State Models of gene regulatory networksAn all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.On the polymer physics origins of protein folding thermodynamics.Quantitative theory of hydrophobic effect as a driving force of protein structureElectronic polarization stabilizes tertiary structure prediction of HP-36.A test on peptide stability of AMBER force fields with implicit solvationBlind test of physics-based prediction of protein structures.Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms.Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.Sampling the multiple folding mechanisms of Trp-cage in explicit solventSrc kinase conformational activation: thermodynamics, pathways, and mechanisms.Chemical, physical, and theoretical kinetics of an ultrafast folding protein.Quantitative determination of site-specific conformational distributions in an unfolded protein by solid-state nuclear magnetic resonance.Folding simulations of a de novo designed protein with a betaalphabeta fold.Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.Enhanced sampling and applications in protein folding in explicit solvent.Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Pathways for virus assembly around nucleic acids.Network models for molecular kinetics and their initial applications to human healthFolding network of villin headpiece subdomain.Challenges in protein folding simulations: Timescale, representation, and analysisHeterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpieceInsights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations.The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnelUnderstanding ensemble protein folding at atomic detailSystematically constructing kinetic transition network in polypeptide from top to down: trajectory mapping.On the characterization of protein native state ensembles.Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulationsLocal structure formation in simulations of two small proteins.Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithmAll-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations
P2860
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P2860
Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece
description
2006 nî lūn-bûn
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2006 թուականի Ապրիլին հրատարակուած գիտական յօդուած
@hyw
2006 թվականի ապրիլին հրատարակված գիտական հոդված
@hy
2006年の論文
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2006年論文
@yue
2006年論文
@zh-hant
2006年論文
@zh-hk
2006年論文
@zh-mo
2006年論文
@zh-tw
2006年论文
@wuu
name
Using massively parallel simul ...... namics of the villin headpiece
@ast
Using massively parallel simul ...... namics of the villin headpiece
@en
Using massively parallel simul ...... namics of the villin headpiece
@nl
type
label
Using massively parallel simul ...... namics of the villin headpiece
@ast
Using massively parallel simul ...... namics of the villin headpiece
@en
Using massively parallel simul ...... namics of the villin headpiece
@nl
prefLabel
Using massively parallel simul ...... namics of the villin headpiece
@ast
Using massively parallel simul ...... namics of the villin headpiece
@en
Using massively parallel simul ...... namics of the villin headpiece
@nl
P2093
P2860
P3181
P356
P1476
Using massively parallel simul ...... namics of the villin headpiece
@en
P2093
Guha Jayachandran
Vijay S Pande
P2860
P304
P3181
P356
10.1063/1.2186317
P407
P577
2006-04-28T00:00:00Z