Deflation reveals dynamical structure in nondominant reaction coordinates

Identification of kinetic order parameters for non-equilibrium dynamics

(2019) Fabian Paul et al.   JOURNAL OF CHEMICAL PHYSICS

Variational selection of features for molecular kinetics

(2019) Martin K. Scherer 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

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

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

(2017) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

A critical appraisal of Markov state models

(2015) Ch. Schütte et al.   European Physical Journal-Special Topics

Nonparametric variational optimization of reaction coordinates

(2015) Polina V. Banushkina et al.   JOURNAL OF CHEMICAL PHYSICS

Variational cross-validation of slow dynamical modes in molecular kinetics

(2015) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

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

Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1

(2012) Tatyana Krivobokova et al.   BIOPHYSICAL JOURNAL

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

How Fast-Folding Proteins Fold

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

Detection of Functional Modes in Protein Dynamics

(2009) Jochen S. Hub et al.   PLoS Computational Biology