Transition networks for modeling the kinetics of conformational change in macromolecules.
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Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15Everything you wanted to know about Markov State Models but were afraid to askTaming the complexity of protein foldingMolecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'Markov state model reveals folding and functional dynamics in ultra-long MD trajectoriesPrinciples and Overview of Sampling Methods for Modeling Macromolecular Structure and DynamicsA Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription ElongationBridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residueThe free energy landscape of small molecule unbindingThe energy landscape, folding pathways and the kinetics of a knotted proteinExploring the free energy landscape: from dynamics to networks and backA role for both conformational selection and induced fit in ligand binding by the LAO proteinQuantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysisUsing Markov state models to study self-assemblySlow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experimentA simple model predicts experimental folding rates and a hub-like topologyGROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.A network of molecular switches controls the activation of the two-component response regulator NtrC.Structural mechanism of the ATP-induced dissociation of rigor myosin from actinComplete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.Enhanced modeling via network theory: Adaptive sampling of Markov state models.Energy landscapes for a machine learning application to series data.Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data.Rapid equilibrium sampling initiated from nonequilibrium dataProtein folded states are kinetic hubs.Network models for molecular kinetics and their initial applications to human healthKinetic rate constant prediction supports the conformational selection mechanism of protein binding.Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulationsMolecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules.Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experimentsEquilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites.Quantitative analysis of ligand migration from transition networksPredicting the Kinetics of RNA Oligonucleotides Using Markov State Models.Building Markov state models with solvent dynamics.Persistent topology and metastable state in conformational dynamics.A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experimentsComputational study of the "DFG-flip" conformational transition in c-Abl and c-Src tyrosine kinases.
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P2860
Transition networks for modeling the kinetics of conformational change in macromolecules.
description
article científic
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article scientifique
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articolo scientifico
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artigo científico
@pt
bilimsel makale
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scientific article published on April 2008
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vedecký článok
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vetenskaplig artikel
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videnskabelig artikel
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vědecký článek
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name
Transition networks for modeling the kinetics of conformational change in macromolecules.
@en
Transition networks for modeling the kinetics of conformational change in macromolecules.
@nl
type
label
Transition networks for modeling the kinetics of conformational change in macromolecules.
@en
Transition networks for modeling the kinetics of conformational change in macromolecules.
@nl
prefLabel
Transition networks for modeling the kinetics of conformational change in macromolecules.
@en
Transition networks for modeling the kinetics of conformational change in macromolecules.
@nl
P1476
Transition networks for modeling the kinetics of conformational change in macromolecules.
@en
P2093
Stefan Fischer
P304
P356
10.1016/J.SBI.2008.01.008
P577
2008-04-01T00:00:00Z