Related references
Note: Only part of the references are listed.Structure determination of high-energy states in a dynamic protein ensemble
John B. Stiller et al.
NATURE (2022)
NMR spectroscopy captures the essential role of dynamics in regulating biomolecular function
T. Reid Alderson et al.
CELL (2021)
Mechanism of Coupled Folding-upon-Binding of an Intrinsically Disordered Protein
Paul Robustelli et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
Single-molecule FRET methods to study the dynamics of proteins at work
Hisham Mazal et al.
CURRENT OPINION IN BIOMEDICAL ENGINEERING (2019)
Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments
Jithender G. Reddy et al.
JOURNAL OF BIOMOLECULAR NMR (2018)
Complete Coupled Binding-Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling
Andrew P. Collins et al.
BIOCHEMISTRY (2018)
Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations
Fabian Paul et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding
Yunhui Ge et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2018)
Molecular Dynamics-Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit
Kelly M. Thayer et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Nuria Plattner et al.
NATURE CHEMISTRY (2017)
Combining experimental and simulation data of molecular processes via augmented Markov models
Simon Olsson et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Fabian Paul et al.
NATURE COMMUNICATIONS (2017)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models
Guangfeng Zhou et al.
BIOPHYSICAL JOURNAL (2017)
The drug-target residence time model: a 10-year retrospective
Robert A. Copeland
NATURE REVIEWS DRUG DISCOVERY (2016)
Allosteric switch regulates protein-protein binding through collective motion
Colin A. Smith et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis
Kalyan S. Chakrabarti et al.
CELL REPORTS (2016)
How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates
Fabian Paul et al.
PLOS COMPUTATIONAL BIOLOGY (2016)
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
Robert T. McGibbon et al.
BIOPHYSICAL JOURNAL (2015)
Estimation and uncertainty of reversible Markov models
Benjamin Trendelkamp-Schroer et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
Sarah Rauscher et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
Martin K. Scherer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Visualizing the Molecular Recognition Trajectory of an Intrinsically Disordered Protein Using Multinuclear Relaxation Dispersion NMR
Robert Schneider et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
Nuria Plattner et al.
NATURE COMMUNICATIONS (2015)
Essential role of conformational selection in ligand binding
Austin D. Vogt et al.
BIOPHYSICAL CHEMISTRY (2014)
Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
Robert B. Best et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Conformational selection in protein binding and function
Thomas R. Weikl et al.
PROTEIN SCIENCE (2014)
Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
Shuo Gu et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
Christian R. Schwantes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Fuzzy spectral clustering by PCCA plus : application to Markov state models and data classification
Susanna Roeblitz et al.
ADVANCES IN DATA ANALYSIS AND CLASSIFICATION (2013)
Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism
Austin D. Vogt et al.
BIOCHEMISTRY (2012)
REFMAC5 for the refinement of macromolecular crystal structures
Garib N. Murshudov et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2011)
Making Ends Meet: The Importance of the N- and C-Termini for the Structure, Stability, and Function of the Third SH3 Domain of CIN85
D. Philippe et al.
BIOCHEMISTRY (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
Guillaume Bouvignies et al.
NATURE (2011)
The structure of human ubiquitin in 2-methyl-2,4-pentanediol: A new conformational switch
Kuo Ying Huang et al.
PROTEIN SCIENCE (2011)
A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
Daniel-Adriano Silva et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
XDS
Wolfgang Kabsch
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)
Features and development of Coot
P. Emsley et al.
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)
Chemical Synthesis of Ubiquitin, Ubiquitin-Based Probes, and Diubiquitin
Farid El Oualid et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)
Everything you wanted to know about Markov State Models but were afraid to ask
Vijay S. Pande et al.
METHODS (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Theory, Practice, and Applications of Paramagnetic Relaxation Enhancement for the Characterization of Transient Low-Population States of Biological Macromolecules and Their Complexes
G. Marius Clore et al.
CHEMICAL REVIEWS (2009)
Progress and challenges in the automated construction of Markov state models for full protein systems
Gregory R. Bowman et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
TRANSITION PATH THEORY FOR MARKOV JUMP PROCESSES
Philipp Metzner et al.
MULTISCALE MODELING & SIMULATION (2009)
The role of dynamic conformational ensembles in biomolecular recognition
David D. Boehr et al.
NATURE CHEMICAL BIOLOGY (2009)
Conformational selection or induced fit: A flux description of reaction mechanism
Gordon G. Hammes et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Characterization of enzyme motions by solution NMR relaxation dispersion
J. Patrick Loria et al.
ACCOUNTS OF CHEMICAL RESEARCH (2008)
Interactions between the three CIN85SH3 domains and ubiquitin: Implications for CIN85 ubiquitination
Irina Bezsonova et al.
BIOCHEMISTRY (2008)
Coarse master equations for peptide folding dynamics
Nicolae-Viorel Buchete et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection
Sarah M. Sullivan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
Oliver F. Lange et al.
SCIENCE (2008)
Dynamic personalities of proteins
Katherine Henzler-Wildman et al.
NATURE (2007)
Structural basis for ubiquitin recognition by SH3 domains
Yuan He et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Phaser crystallographic software
Airlie J. McCoy et al.
JOURNAL OF APPLIED CRYSTALLOGRAPHY (2007)
Mechanism of coupled folding and binding of an intrinsically disordered protein
Kenji Sugase et al.
NATURE (2007)
Observation of μs time-scale protein dynamics in the presence of Ln3+stop ions:: application to the N-terminal domain of cardiac troponin C
Christian Eichmueller et al.
JOURNAL OF BIOMOLECULAR NMR (2007)
Canonical sampling through velocity rescaling
Giovanni Bussi et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
The dynamic energy landscape of dihydrofolate reductase catalysis
David D. Boehr et al.
SCIENCE (2006)
An NMR perspective on enzyme dynamics
David D. Boehr et al.
CHEMICAL REVIEWS (2006)
Towards a theory of transition paths
Weinan E et al.
JOURNAL OF STATISTICAL PHYSICS (2006)
Review - New tools provide new insights in NMR studies of protein dynamics
A Mittermaier et al.
SCIENCE (2006)
NMR characterization of the dynamics of biomacromolecules
AG Palmer
CHEMICAL REVIEWS (2004)
Antibody multispecificity mediated by conformational diversity
LC James et al.
SCIENCE (2003)
Absolute comparison of simulated and experimental protein-folding dynamics
CD Snow et al.
NATURE (2002)
Studying excited states of proteins by NMR spectroscopy
FAA Mulder et al.
NATURE STRUCTURAL BIOLOGY (2001)
Share Paper
