Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

(2019) Jiang Wang et al.   ACS Central Science

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

Tinker 8: Software Tools for Molecular Design

(2018) Joshua A. Rackers et al.   Journal of Chemical Theory and Computation

ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost

(2017) J. S. Smith et al.   Chemical Science

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

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Deep learning

(2015) Yann LeCun et al.   NATURE

Locating landmarks on high-dimensional free energy surfaces

(2015) Ming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Density estimation by dual ascent of the log-likelihood

(2013) Esteban G. Tabak et al.   Communications in Mathematical Sciences

Identification of slow molecular order parameters for Markov model construction

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

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

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

Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

(2012) Matthias Rupp et al.   PHYSICAL REVIEW LETTERS

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation

(2011) J. P. Nilmeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS