A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories. - Tiankai Tu; Charles A. Rendleman; David W. Borhani; Ron O. Dror; Justin Gullingsrud; Morten Ø. Jensen; John L. Klepeis; Paul Maragakis; Patrick J. Miller; Kate A. Stafford; David E. Shaw (SC, 2008)

Millisecond-scale molecular dynamics simulations on Anton. - David E. Shaw; Ron O. Dror; John K. Salmon; J. P. Grossman; Kenneth M. Mackenzie; Joseph A. Bank; Cliff Young; Martin M. Deneroff; Brannon Batson; Kevin J. Bowers; Edmond Chow; Michael P. Eastwood; et al. (SC, 2009)

A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. - Paul Maragakis; Hunter M. Nisonoff; Brian Cole; David E. Shaw (J. Chem. Inf. Model., 2020)

Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. - Jack B. Greisman; Lindsay Willmore; Christine Y. Yeh; Fabrizio Giordanetto; Sahar Shahamadtar; Hunter M. Nisonoff; Paul Maragakis; David E. Shaw (J. Chem. Inf. Model., 2023)

A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. - Christine Y. Yeh; Jesus A. Izaguirre; Jack B. Greisman; Lindsay Willmore; Paul Maragakis; David E. Shaw (J. Chem. Inf. Model., 2023)