Girsanov reweighting for metadynamics simulations

Metadynamics Enhanced Markov Modeling of Protein Dynamics

(2018) Mithun Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

An Automatic Adaptive Importance Sampling Algorithm for Molecular Dynamics in Reaction Coordinates

(2018) J. Quer et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Girsanov reweighting for path ensembles and Markov state models

(2017) L. Donati et al.   JOURNAL OF CHEMICAL PHYSICS

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

(2017) Rodrigo Casasnovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States

(2016) Jagna Witek et al.   Journal of Chemical Information and Modeling

Density-based cluster algorithms for the identification of core sets

(2016) Oliver Lemke et al.   JOURNAL OF CHEMICAL PHYSICS

Multiensemble Markov models of molecular thermodynamics and kinetics

(2016) Hao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier 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

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

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

(2014) Edina Rosta et al.   Journal of Chemical Theory and Computation

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov state models and molecular alchemy

(2014) Christof Schütte et al.   MOLECULAR PHYSICS

Kinetic modulation of a disordered protein domain by phosphorylation

(2014) Nathaniel Stanley et al.   Nature Communications

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández 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

From Metadynamics to Dynamics

(2013) Pratyush Tiwary et al.   PHYSICAL REVIEW LETTERS

Requirement of Ca2+ Ions for the Hyperthermostability of Tk-Subtilisin from Thermococcus kodakarensis

(2012) Ryo Uehara et al.   BIOCHEMISTRY

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

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 state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

(2011) Bettina Keller et al.   Journal of Chemical Theory and Computation

Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations

(2010) Pietro Faccioli et al.   JOURNAL OF CHEMICAL PHYSICS

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

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multidimensional Langevin modeling of biomolecular dynamics

(2009) Rainer Hegger et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

(2009) David D. L. Minh et al.   JOURNAL OF CHEMICAL PHYSICS

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Coarse Master Equations for Peptide Folding Dynamics†

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS