Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

(2018) João Marcelo Lamim Ribeiro et al.   JOURNAL OF CHEMICAL PHYSICS

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

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer 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

Data-Driven Model Reduction and Transfer Operator Approximation

(2018) Stefan Klus et al.   JOURNAL OF NONLINEAR SCIENCE

Markov State Models: From an Art to a Science

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

Recruiting machine learning methods for molecular simulations of proteins

(2018) Shriyaa Mittal et al.   MOLECULAR SIMULATION

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

NSF’s Inaugural Software Institutes: The Science Gateways Community Institute and the Molecular Sciences Software Institute

(2018) Nancy Wilkins-Diehr et al.   COMPUTING IN SCIENCE & ENGINEERING

Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes

(2018) Zahra Shamsi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science

(2018) Anna Krylov et al.   JOURNAL OF CHEMICAL PHYSICS

Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE

(2018) João Marcelo Lamim Ribeiro et al.   Journal of Chemical Theory and Computation

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

Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems

(2016) Guillermo Pérez-Hernández et al.   Journal of Chemical Theory and Computation

Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling

(2016) Frank Noé et al.   Journal of Chemical Theory and Computation

Estimation and uncertainty of reversible Markov models

(2015) Benjamin Trendelkamp-Schroer 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

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

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

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates

(2014) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

Variational Approach to Molecular Kinetics

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

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations

(2014) S. Doerr et al.   Journal of Chemical Theory and Computation

Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics

(2014) Jordane Preto et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

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

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

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

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

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

(2011) Andrew L. Ferguson et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies

(2011) Jeffrey K. Weber et al.   Journal of Chemical Theory and Computation

How Fast-Folding Proteins Fold

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

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

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

(2009) Hernán Stamati et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS