An efficient Bayesian kinetic lumping algorithm to identify metastable conformational states via Gibbs sampling

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

(2017) Wei Wang et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Variational Identification of Markovian Transition States

(2017) Linda Martini et al.   Physical Review X

Robust Density-Based Clustering To Identify Metastable Conformational States of Proteins

(2016) Florian Sittel et al.   Journal of Chemical Theory and Computation

Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories

(2016) Song Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit

(2016) Bin W. Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

(2016) Lin-Tai Da et al.   Nature Communications

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

(2015) Toshifumi Mori et al.   JOURNAL OF CHEMICAL PHYSICS

Estimation and uncertainty of reversible Markov models

(2015) Benjamin Trendelkamp-Schroer et al.   JOURNAL OF CHEMICAL PHYSICS

Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps

(2015) Lorenzo Boninsegna et al.   Journal of Chemical Theory and Computation

Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems

(2014) Fu Kit Sheong et al.   Journal of Chemical Theory and Computation

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

(2014) Robert D. Malmstrom et al.   Journal of Chemical Theory and Computation

Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering

(2014) Abhinav Jain et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models

(2014) Gerhard Hummer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales

(2013) Benjamin Schuler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Quantitative comparison of alternative methods for coarse-graining biological networks

(2013) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Consensus for the Fip35 folding mechanism?

(2013) Ganna Berezovska et al.   JOURNAL OF CHEMICAL PHYSICS

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

(2013) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

(2013) Yuan Yao et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics

(2013) Robert T. McGibbon 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

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

(2012) Gregory R. Bowman   JOURNAL OF CHEMICAL PHYSICS

Identifying Metastable States of Folding Proteins

(2012) Abhinav Jain et al.   Journal of Chemical Theory and Computation

A fast parallel clustering algorithm for molecular simulation trajectories

(2012) Yutong Zhao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics

(2011) Sergei V. Krivov   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

(2010) Faruck Morcos et al.   PLoS Computational Biology

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

(2009) Sergio Bacallado et al.   JOURNAL OF CHEMICAL PHYSICS

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Ten-Microsecond Molecular Dynamics Simulation of a Fast-Folding WW Domain

(2008) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An experimental survey of the transition between two-state and downhill protein folding scenarios

(2008) F. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA