Supercomputing in biology: towards understanding living systems in atomic detail. - Karissa Y. Sanbonmatsu (SIGSOFT FSE, 2010)

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)

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)

A magnesium-induced triplex pre-organizes the SAM-II riboswitch. - Susmita Roy; Heiko Lammert; Ryan L. Hayes; Bin Chen; Regan LeBlanc; T. Kwaku Dayie; José N. Onuchic; Karissa Y. Sanbonmatsu (PLoS Comput. Biol., 2017)

Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations. - Jaewoon Jung; Wataru Nishima; Marcus Daniels; Gavin Bascom; Chigusa Kobayashi; Adetokunbo Adedoyin; Michael E. Wall; Anna Lappala; Dominic Phillips; William Fischer 001; Chang-Shung Tung; Tamar Schlick; et al. (J. Comput. Chem., 2019)

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps. - Doo Nam Kim; Dominik Gront; Karissa Y. Sanbonmatsu (J. Chem. Inf. Model., 2020)

Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein. - Dylan Girodat; Avik K. Pati; Daniel S. Terry; Scott C. Blanchard; Karissa Y. Sanbonmatsu (PLoS Comput. Biol., 2020)