Diffusive reaction dynamics on invariant free energy profiles.
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Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsThe free energy landscape of small molecule unbindingConnecting the kinetics and energy landscape of tRNA translocation on the ribosomeAnalysis of the free-energy surface of proteins from reversible folding simulations.Data-driven approach to decomposing complex enzyme kinetics with surrogate models.Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles.Gaussian-mixture umbrella sampling.Coordinate-dependent diffusion in protein folding.Is protein folding sub-diffusive?Testing for memory-free spectroscopic coordinates by 3D IR exchange spectroscopyThe origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein foldingRecent developments in methods for identifying reaction coordinates.Challenges in protein folding simulations: Timescale, representation, and analysisFree energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.Capturing transition paths and transition states for conformational rearrangements in the ribosome.Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant.Peptide Binding to a PDZ Domain by Electrostatic Steering via Nonnative Salt Bridges.Diffusion models of protein foldingQuantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy.Localizing internal friction along the reaction coordinate of protein folding by combining ensemble and single-molecule fluorescence spectroscopyFree energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulationsCalculation of free-energy differences by confinement simulations. Application to peptide conformersObservation time scale, free-energy landscapes, and molecular symmetry.The role of high-dimensional diffusive search, stabilization, and frustration in protein folding.Contact- and distance-based principal component analysis of protein dynamics.Modulation of a protein free-energy landscape by circular permutation.Fisher information metric for the Langevin equation and least informative models of continuous stochastic dynamics.How the diffusivity profile reduces the arbitrariness of protein folding free energies.Method to describe stochastic dynamics using an optimal coordinate.Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency.Peptide binding to the PDZ3 domain by conformational selection.Interplay of fast and slow dynamics in rare transition pathways: The disk-to-slab transition in the 2d Ising model.Decoding the energy landscape: extracting structure, dynamics and thermodynamics.Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape.Identification of the protein folding transition state from molecular dynamics trajectories.Nonparametric variational optimization of reaction coordinates.Fep1d: a script for the analysis of reaction coordinates.Energy landscapes and persistent minima.Nonequilibrium NMR Methods for Monitoring Protein and RNA FoldingNew advances in metadynamics
P2860
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P2860
Diffusive reaction dynamics on invariant free energy profiles.
description
2008 nî lūn-bûn
@nan
2008年の論文
@ja
2008年論文
@yue
2008年論文
@zh-hant
2008年論文
@zh-hk
2008年論文
@zh-mo
2008年論文
@zh-tw
2008年论文
@wuu
2008年论文
@zh
2008年论文
@zh-cn
name
Diffusive reaction dynamics on invariant free energy profiles.
@en
type
label
Diffusive reaction dynamics on invariant free energy profiles.
@en
prefLabel
Diffusive reaction dynamics on invariant free energy profiles.
@en
P2860
P356
P1476
Diffusive reaction dynamics on invariant free energy profiles.
@en
P2093
Sergei V Krivov
P2860
P304
13841-13846
P356
10.1073/PNAS.0800228105
P407
P577
2008-09-04T00:00:00Z