Deep clustering of protein folding simulations

An automated analysis workflow for optimization of force-field parameters using neutron scattering data

(2017) Vickie E. Lynch et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Computational ‘microscopy’ of cellular membranes

(2016) Helgi I. Ingólfsson et al.   JOURNAL OF CELL SCIENCE

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study

(2016) Gurpreet K. Dhindsa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2015) Sang Beom Kim et al.   JOURNAL OF CHEMICAL PHYSICS

Deep Learning in Drug Discovery

(2015) Erik Gawehn et al.   Molecular Informatics

Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins

(2014) Andrej J. Savol et al.   Journal of Chemical Theory and Computation

Protein Conformational Populations and Functionally Relevant Substates

(2013) Arvind Ramanathan et al.   ACCOUNTS OF CHEMICAL RESEARCH

Evaluation of Dimensionality-Reduction Methods from Peptide Folding–Unfolding Simulations

(2013) Mojie Duan et al.   Journal of Chemical Theory and Computation

Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: Application to enzyme adenylate kinase

(2013) Arvind Ramanathan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

On-the-Fly Identification of Conformational Substates from Molecular Dynamics Simulations

(2011) Arvind Ramanathan et al.   Journal of Chemical Theory and Computation

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovering Conformational Sub-States Relevant to Protein Function

(2011) Arvind Ramanathan et al.   PLoS One

How Fast-Folding Proteins Fold

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

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY