Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
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Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsPolymer uncrossing and knotting in protein folding, and their role in minimal folding pathwaysPath Similarity Analysis: A Method for Quantifying Macromolecular PathwaysZipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.Equilibrium sampling for biomolecules under mechanical tensionGaussian-mixture umbrella sampling.A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy ProfilesCy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.Hysteresis-based mechanism for the directed motility of the Ncd motor.Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations.Finding transition pathways using the string method with swarms of trajectories.String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting StateConformational transition pathways explored by Monte Carlo simulation integrated with collective modes.Beyond microscopic reversibility: Are observable non-equilibrium processes precisely reversible?Steady-state simulations using weighted ensemble path sampling.Vibrational dynamics of azide-derivatized amino acids studied by nonlinear infrared spectroscopy.Path finding on high-dimensional free energy landscapes.Sampling large conformational transitions: adenylate kinase as a testing ground
P2860
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P2860
Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
description
2007 nî lūn-bûn
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2007年の論文
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2007年学术文章
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name
Minimum free energy pathways a ...... olecular dynamics simulations.
@en
Minimum free energy pathways a ...... olecular dynamics simulations.
@nl
type
label
Minimum free energy pathways a ...... olecular dynamics simulations.
@en
Minimum free energy pathways a ...... olecular dynamics simulations.
@nl
prefLabel
Minimum free energy pathways a ...... olecular dynamics simulations.
@en
Minimum free energy pathways a ...... olecular dynamics simulations.
@nl
P2860
P356
P1476
Minimum free energy pathways a ...... olecular dynamics simulations.
@en
P2093
Arjan van der Vaart
P2860
P304
P356
10.1063/1.2719697
P407
P577
2007-04-01T00:00:00Z