SMOG@ctbp: simplified deployment of structure-based models in GROMACS. - Jeffrey K. Noel; Paul C. Whitford; Karissa Y. Sanbonmatsu; José N. Onuchic (Nucleic Acids Res., 2010)

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function. - Michael A. Jamros; Leandro C. Oliveira; Paul C. Whitford; José N. Onuchic; Joseph A. Adams; Patricia A. Jennings (PLoS Comput. Biol., 2012)

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome. - Paul C. Whitford; Scott C. Blanchard; Jamie H. D. Cate; Karissa Y. Sanbonmatsu (PLoS Comput. Biol., 2013)

SMOG 2: A Versatile Software Package for Generating Structure-Based Models. - Jeffrey K. Noel; Mariana Levi; Mohit Raghunathan; Heiko Lammert; Ryan L. Hayes; José N. Onuchic; Paul C. Whitford (PLoS Comput. Biol., 2016)

Structure-Function Dynamics Hybrid Modeling: RNA Degradation. - Hua Zheng; Wei Xie; Chunsheng Fang; Wandi Xu; Paul C. Whitford; Ailun Wang (WSC, 2023)