Enspara: Modeling molecular ensembles with scalable data structures and parallel computing

Complete Coupled Binding–Folding Pathway of the Intrinsically Disordered Transcription Factor Protein Brinker Revealed by Molecular Dynamics Simulations and Markov State Modeling

(2018) Andrew P. Collins et al.   BIOCHEMISTRY

Markov State Models: From an Art to a Science

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

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

(2018) Wei Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

(2018) Xianqiang Sun et al.   eLife

Peptide dimerization-dissociation rates from replica exchange molecular dynamics

(2017) Cathal T. Leahy et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetics from Replica Exchange Molecular Dynamics Simulations

(2017) Lukas S. Stelzl et al.   Journal of Chemical Theory and Computation

Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS

(2017) Sukrit Singh et al.   Journal of Chemical Theory and Computation

Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models

(2017) Maxwell I. Zimmerman et al.   ACS Central Science

Modelling proteins’ hidden conformations to predict antibiotic resistance

(2016) Kathryn M. Hart et al.   Nature Communications

Efficient Estimation of Rare-Event Kinetics

(2016) Benjamin Trendelkamp-Schroer et al.   Physical Review X

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Projected metastable Markov processes and their estimation with observable operator models

(2015) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling Molecular Kinetics with tICA and the Kernel Trick

(2015) Christian R. Schwantes 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

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

(2015) Gregory R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Extensive Conformational Heterogeneity within Protein Cores

(2014) Gregory R. Bowman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution

(2013) Benjamin Trendelkamp-Schroer 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

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

(2013) Frank Noé et al.   JOURNAL OF CHEMICAL PHYSICS

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

Optimal simultaneous superpositioning of multiple structures with missing data

(2012) Douglas L. Theobald et al.   BIOINFORMATICS

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A fast parallel clustering algorithm for molecular simulation trajectories

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

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel distributed computing using Python

(2011) Lisandro D. Dalcin et al.   ADVANCES IN WATER RESOURCES

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi 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

A supervised clustering approach for fMRI-based inference of brain states

(2011) Vincent Michel et al.   PATTERN RECOGNITION

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

(2011) F. Noe 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

Cython: The Best of Both Worlds

(2010) Stefan Behnel et al.   COMPUTING IN SCIENCE & ENGINEERING

Hidden Complexity of Protein Free-Energy Landscapes Revealed by Principal Component Analysis by Parts

(2010) Abhinav Jain et al.   Journal of Physical Chemistry Letters

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

(2010) Vijay S. Pande et al.   METHODS

Protein folded states are kinetic hubs

(2010) G. R. Bowman 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

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

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

(2009) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

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

(2009) Gregory R. Bowman et al.   METHODS

Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data

(2009) Philipp Metzner et al.   PHYSICAL REVIEW E

Coarse Master Equations for Peptide Folding Dynamics†

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

MPI for Python: Performance improvements and MPI-2 extensions

(2007) Lisandro Dalcín et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING