State predictive information bottleneck

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide

(2020) Yusuke Mori et al.   JOURNAL OF CHEMICAL PHYSICS

Galerkin approximation of dynamical quantities using trajectory data

(2019) Erik H. Thiede et al.   JOURNAL OF CHEMICAL PHYSICS

Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics

(2019) Yihang Wang et al.   Nature Communications

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

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

Metadynamics Enhanced Markov Modeling of Protein Dynamics

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

Author Correction: VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Reaction Coordinates and Mechanistic Hypothesis Tests

(2016) Baron Peters   Annual Review of Physical Chemistry

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

(2016) Santanu Roy et al.   Journal of Physical Chemistry C

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

Dependence of the Rate of LiF Ion-Pairing on the Description of Molecular Interaction

(2015) Eva Pluhařová et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PLUMED 2: New feathers for an old bird

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

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

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

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Calculating rate constants and committor probabilities for transition networks by graph transformation

(2009) David J. Wales   JOURNAL OF CHEMICAL PHYSICS

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION