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

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method

(2017) Andrew L. Ferguson   JOURNAL OF COMPUTATIONAL CHEMISTRY

Machine learning and data science in soft materials engineering

(2017) Andrew L Ferguson   JOURNAL OF PHYSICS-CONDENSED MATTER

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

(2017) Eliodoro Chiavazzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Topological obstructions in the way of data-driven collective variables

(2015) Behrooz Hashemian et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic characterization of protein folding pathways using diffusion maps: Application to Trp-cage miniprotein

(2015) Sang Beom Kim 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

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

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

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

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

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

(2013) Cameron Abrams et al.   Entropy

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

(2013) Behrooz Hashemian et al.   JOURNAL OF CHEMICAL PHYSICS

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

How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

(2013) Nan-jie Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics

(2013) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

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

On-the-fly free energy parameterization via temperature accelerated molecular dynamics

(2012) Cameron F. Abrams et al.   CHEMICAL PHYSICS LETTERS

Variation of conformational properties at a glance. True graphical visualization of the Ramachandran surface topology as a periodic potential energy surface

(2012) Imre Jákli et al.   CHEMICAL PHYSICS LETTERS

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

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

Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach

(2011) Andrew L. Ferguson et al.   CHEMICAL PHYSICS LETTERS

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

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

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

(2011) Vojtěch Spiwok et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

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

Quantifying Density Fluctuations in Volumes of All Shapes and Sizes Using Indirect Umbrella Sampling

(2011) Amish J. Patel et al.   JOURNAL OF STATISTICAL PHYSICS

An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25

(2010) Andrew L. Ferguson et al.   BIOPHYSICAL JOURNAL

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins

(2009) Pavel I. Zhuravlev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

(2008) Jerry B. Abrams 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

Computing the stability diagram of the Trp-cage miniprotein

(2008) D. Paschek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA