OSPREY 3.0: Open-source protein redesign for you, with powerful new features. - Mark A. Hallen; Jeffrey W. Martin; Adegoke A. Ojewole; Jonathan D. Jou; Anna U. Lowegard; Marcel S. Frenkel; Pablo Gainza; Hunter M. Nisonoff; Aditya Mukund; Siyu Wang; Graham T. Holt; David Zhou; et al. (J. Comput. Chem., 2018)

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)