Automated design of collective variables using supervised machine learning

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

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

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics

(2018) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

A variational conformational dynamics approach to the selection of collective variables in metadynamics

(2017) James McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling the mechanism of CLN025 beta-hairpin formation

(2017) Keri A. McKiernan et al.   JOURNAL OF CHEMICAL PHYSICS

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

(2017) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems

(2017) Mohammad M. Sultan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

(2017) Mohammad M. Sultan et al.   Scientific Reports

Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations

(2016) Sunhwan Jo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A structural approach to relaxation in glassy liquids

(2016) S. S. Schoenholz et al.   Nature Physics

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases

(2015) Yilin Meng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations

(2014) Mohammad M. Sultan 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

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

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

PLUMED 2: New feathers for an old bird

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

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Identification of slow molecular order parameters for Markov model construction

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

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

(2013) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Optimizing transition states via kernel-based machine learning

(2012) Zachary D. Pozun et al.   JOURNAL OF CHEMICAL PHYSICS

The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation

(2012) Silvia Lovera et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2010) Vijay S. Pande et al.   METHODS

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Kernel methods in machine learning

(2008) Thomas Hofmann et al.   ANNALS OF STATISTICS

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystal Structure of a Ten-Amino Acid Protein

(2008) Shinya Honda et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS