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

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models

(2016) Lu Zhang et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

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

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

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

A Basis Set for Peptides for the Variational Approach to Conformational Kinetics

(2015) F. Vitalini et al.   Journal of Chemical Theory and Computation

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs

(2015) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement

(2015) Hanlun Jiang et al.   PLoS Computational Biology

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske 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

Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models

(2014) Vincent A. Voelz et al.   Journal of Chemical Theory and Computation

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

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

(2014) Shuo Gu et al.   PLoS Computational Biology

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

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

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

(2013) Lin-Tai Da et al.   PLoS Computational Biology

A fast parallel clustering algorithm for molecular simulation trajectories

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

Markov models of molecular kinetics: Generation and validation

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

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

Taming the complexity of protein folding

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

Comparing geometric and kinetic cluster algorithms for molecular simulation data

(2010) Bettina Keller et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW

(2010) Faruck Morcos et al.   PLoS Computational Biology

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

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

A simple and fast algorithm for K-medoids clustering

(2008) Hae-Sang Park et al.   EXPERT SYSTEMS WITH APPLICATIONS

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

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

Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding†

(2008) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse Master Equations for Peptide Folding Dynamics†

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