(Q46474092)

22 December 2017

title

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics (English)

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22 December 2017

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Vijay S Pande

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22 December 2017

Ken A. Dill

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object named as

Ken A Dill

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22 December 2017

author name string

John D Chodera

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22 December 2017

Nina Singhal

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22 December 2017

William C Swope

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22 December 2017

language of work or name

English

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publication date

1 April 2007

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22 December 2017

Journal of Chemical Physics

published in

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22 December 2017

volume

126

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22 December 2017

issue

15

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22 December 2017

page(s)

155101

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22 December 2017

Protein folding and misfolding

cites work

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Allosteric modulation bypasses the requirement for ATP hydrolysis in regenerating low affinity transition state conformation of human P-glycoprotein

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One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions

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Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

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Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

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Protein folding pathways from replica exchange simulations and a kinetic network model

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Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

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Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

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Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data

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Error analysis and efficient sampling in Markovian state models for molecular dynamics.

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Foldamer dynamics expressed via Markov state models. II. State space decomposition

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Validation of Markov state models using Shannon's entropy.

21 January 2018

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Protein states and proteinquakes

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Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

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Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

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Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

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COMPUTING: Screen Savers of the World Unite!

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

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Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

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Bootstrap Methods: Another Look at the Jackknife

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A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

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Reaction coordinates of biomolecular isomerization

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Automatic method for identifying reaction coordinates in complex systems.

21 January 2018

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Comparison of simple potential functions for simulating liquid water

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

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Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

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Electrostatic screening of charge and dipole interactions with the helix backbone

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Fast events in protein folding: helix melting and formation in a small peptide.

21 January 2018

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Laser temperature jump study of the helix<==>coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model

21 January 2018

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Transient UV Raman spectroscopy finds no crossing barrier between the peptide alpha-helix and fully random coil conformation

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Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

21 January 2018

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Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

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Detection-dependent kinetics as a probe of folding landscape microstructure

21 January 2018

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Tryptophan zippers: Stable, monomeric -hairpins

21 January 2018

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Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide

21 January 2018

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Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

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Current Status of Transition-State Theory

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Molecular dynamics with coupling to an external bath

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Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

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21 January 2018

Identifiers

DOI

10.1063/1.2714538

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22 December 2017

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22 December 2017