Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein. - Ana Damjanovic; Benjamin T. Miller; Torre J. Wenaus; Petar Maksimovic; Bertrand García-Moreno E.; Bernard R. Brooks (J. Chem. Inf. Model., 2008)

CHARMMing: A New, Flexible Web Portal for CHARMM. - Benjamin T. Miller; Rishi P. Singh; Jeffery B. Klauda; Milan Hodoscek; Bernard R. Brooks; H. Lee Woodcock III (J. Chem. Inf. Model., 2008)

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. - Urban Borstnik; Benjamin T. Miller; Bernard R. Brooks; Dusanka Janezic (J. Comput. Chem., 2011)

Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. - An Ghysels; Benjamin T. Miller; Frank C. Pickard IV; Bernard R. Brooks (J. Comput. Chem., 2012)

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. - Benjamin T. Miller; Rishi P. Singh; Vinushka Schalk; Yuri Pevzner; Jingjun Sun; Carrie S. Miller; Stefan Boresch; Toshiko Ichiye; Bernard R. Brooks; H. Lee Woodcock III (PLoS Comput. Biol., 2014)

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. - Bradley Scott Perrin Jr.; Benjamin T. Miller; Vinushka Schalk; H. Lee Woodcock III; Bernard R. Brooks; Toshiko Ichiye (PLoS Comput. Biol., 2014)

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. - Frank C. Pickard IV; Benjamin T. Miller; Vinushka Schalk; Michael G. Lerner; H. Lee Woodcock III; Bernard R. Brooks (PLoS Comput. Biol., 2014)

Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. - Iwona E. Weidlich; Yuri Pevzner; Benjamin T. Miller; Igor V. Filippov; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Chem., 2015)

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. - Janez Konc; Benjamin T. Miller; Tanja Stular; Samo Lesnik; H. Lee Woodcock III; Bernard R. Brooks; Dusanka Janezic (J. Chem. Inf. Model., 2015)