Multiensemble Markov models of molecular thermodynamics and kinetics
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Multiensemble Markov models of molecular thermodynamics and kinetics
Authors
Keywords
-
Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 113, Issue 23, Pages E3221-E3230
Publisher
Proceedings of the National Academy of Sciences
Online
2016-05-26
DOI
10.1073/pnas.1525092113
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Optimally Adjusted Mixture Sampling and Locally Weighted Histogram Analysis
- (2017) Zhiqiang Tan JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
- Estimation and uncertainty of reversible Markov models
- (2015) Benjamin Trendelkamp-Schroer et al. JOURNAL OF CHEMICAL PHYSICS
- Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation
- (2015) Frank Noé et al. Journal of Chemical Theory and Computation
- PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
- (2015) Martin K. Scherer et al. Journal of Chemical Theory and Computation
- A Stochastic Solution to the Unbinned WHAM Equations
- (2015) Bin W. Zhang et al. Journal of Physical Chemistry Letters
- Crystal structure of the dynamin tetramer
- (2015) Thomas F. Reubold et al. NATURE
- Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
- (2015) Pratyush Tiwary et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
- (2015) Nuria Plattner et al. Nature Communications
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
- (2014) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
- (2014) Edina Rosta et al. Journal of Chemical Theory and Computation
- Optimal Estimation of Free Energies and Stationary Densities from Multiple Biased Simulations
- (2014) Hao Wu et al. MULTISCALE MODELING & SIMULATION
- Millisecond dynamics of RNA polymerase II translocation at atomic resolution
- (2014) D.-A. Silva et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Ion permeation in K+ channels occurs by direct Coulomb knock-on
- (2014) D. A. Kopfer et al. SCIENCE
- The Dynamic Process of β2-Adrenergic Receptor Activation
- (2013) Rie Nygaard et al. CELL
- Identification of slow molecular order parameters for Markov model construction
- (2013) Guillermo Pérez-Hernández et al. JOURNAL OF CHEMICAL PHYSICS
- Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions
- (2013) Wojciech Wojtas-Niziurski et al. Journal of Chemical Theory and Computation
- Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
- (2013) James C. Gumbart et al. Journal of Chemical Theory and Computation
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
- (2013) Christian R. Schwantes et al. Journal of Chemical Theory and Computation
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
- (2013) Romelia Salomon-Ferrer et al. Journal of Chemical Theory and Computation
- Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
- (2013) Kai J. Kohlhoff et al. Nature Chemistry
- From Metadynamics to Dynamics
- (2013) Pratyush Tiwary et al. PHYSICAL REVIEW LETTERS
- Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification
- (2013) Susanna Röblitz et al. Advances in Data Analysis and Classification
- Theory of binless multi-state free energy estimation with applications to protein-ligand binding
- (2012) Zhiqiang Tan et al. JOURNAL OF CHEMICAL PHYSICS
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
- (2012) Peter Eastman et al. Journal of Chemical Theory and Computation
- Kinetic characterization of the critical step in HIV-1 protease maturation
- (2012) S. K. Sadiq et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Mechanism of Voltage Gating in Potassium Channels
- (2012) M. O. Jensen et al. SCIENCE
- Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
- (2011) John D. Chodera et al. JOURNAL OF CHEMICAL PHYSICS
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics
- (2011) Jan-Hendrik Prinz et al. JOURNAL OF CHEMICAL PHYSICS
- Markov models of molecular kinetics: Generation and validation
- (2011) Jan-Hendrik Prinz et al. JOURNAL OF CHEMICAL PHYSICS
- Convergence and error estimation in free energy calculations using the weighted histogram analysis method
- (2011) Fangqiang Zhu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Pathway and mechanism of drug binding to G-protein-coupled receptors
- (2011) Ron O. Dror et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
- (2011) I. Buch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
- (2011) Daniel-Adriano Silva et al. PLoS Computational Biology
- High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
- (2010) I. Buch et al. Journal of Chemical Information and Modeling
- Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)
- (2010) Vincent A. Voelz et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85
- (2010) Gregory R. Bowman et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Pore opening and closing of a pentameric ligand-gated ion channel
- (2010) F. Zhu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Atomic-Level Characterization of the Structural Dynamics of Proteins
- (2010) D. E. Shaw et al. SCIENCE
- Membrane-Bending Mechanism of Amphiphysin N-BAR Domains
- (2009) Anton Arkhipov et al. BIOPHYSICAL JOURNAL
- Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages
- (2009) David D. L. Minh et al. JOURNAL OF CHEMICAL PHYSICS
- Progress and challenges in the automated construction of Markov state models for full protein systems
- (2009) Gregory R. Bowman et al. JOURNAL OF CHEMICAL PHYSICS
- ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
- (2009) M. J. Harvey et al. Journal of Chemical Theory and Computation
- Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H
- (2009) Edina Rosta et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
- (2009) Frank Noé et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Residence Time of Receptor−Ligand Complexes and Its Effect on Biological Function
- (2008) Peter J. Tummino et al. BIOCHEMISTRY
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now