Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. - H. Lee Woodcock III; Milan Hodoscek; Andrew T. B. Gilbert; Peter M. W. Gill; Henry F. Schaefer III; Bernard R. Brooks (J. Comput. Chem., 2007)

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)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. - Edina Rosta; H. Lee Woodcock III; Bernard R. Brooks; Gerhard Hummer (J. Comput. Chem., 2009)

Virtual Target Screening: Validation Using Kinase Inhibitors. - Daniel N. Santiago; Yuri Pevzner; Ashley A. Durand; Minh Phuong Tran; Rachel R. Scheerer; Kenyon G. Daniel; Shen-Shu Sung; H. Lee Woodcock III; Wayne C. Guida; Wesley H. Brooks (J. Chem. Inf. Model., 2012)

Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors. - Sai Lakshmana Vankayala; Jacqueline C. Hargis; H. Lee Woodcock III (J. Chem. Inf. Model., 2012)

How Does Catalase Release Nitric Oxide? A Computational Structure-Activity Relationship Study. - Sai Lakshmana Vankayala; Jacqueline C. Hargis; H. Lee Woodcock III (J. Chem. Inf. Model., 2013)

Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle? - Jacqueline C. Hargis; Justin K. White; Yu Chen; H. Lee Woodcock III (J. Chem. Inf. Model., 2014)

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. - Yuri Pevzner; Emilie Frugier; Vinushka Schalk; Amedeo Caflisch; H. Lee Woodcock III (J. Chem. Inf. Model., 2014)

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)

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. - Phillip S. Hudson; Kyungreem Han; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2018)

Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid. - Fiona L. Kearns; Carrie Robart; M. Trent Kemp; Sai Lakshmana Vankayala; Brette M. Chapin; Eric V. Anslyn; H. Lee Woodcock III; Joseph D. Larkin (J. Chem. Inf. Model., 2019)

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. - Phillip S. Hudson; Félix Aviat; Rubén Meana-Pañeda; Luke C. Warrensford; Benjamin C. Pollard; Samarjeet Prasad; Michael R. Jones; H. Lee Woodcock III; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2022)

CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. - Sai Lakshmana Vankayala; Luke C. Warrensford; Amanda R. Pittman; Benjamin C. Pollard; Fiona L. Kearns; Joseph D. Larkin; H. Lee Woodcock III (J. Comput. Chem., 2022)