H. Lee Woodcock III

18 papers Journal 18

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. J. Comput. Chem. Sai Lakshmana Vankayala, Luke C. Warrensford, Amanda R. Pittman, Benjamin C. Pollard, Fiona L. Kearns, Joseph D. Larkin, H. Lee Woodcock III
2022	J	`jnl`	Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid. J. Chem. Inf. Model. Fiona L. Kearns, Carrie Robart, M. Trent Kemp, Sai Lakshmana Vankayala, Brette M. Chapin, Eric V. Anslyn, H. Lee Woodcock III, Joseph D. Larkin
2018	J	`jnl`	Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J. Comput. Aided Mol. Des. Phillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks
2015	J	`jnl`	Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. J. Comput. Chem. Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks
2015	J	`jnl`	ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model. Janez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic
2014	J	`jnl`	Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle? J. Chem. Inf. Model. Jacqueline C. Hargis, Justin K. White, Yu Chen, H. Lee Woodcock III
2014	J	`jnl`	Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J. Chem. Inf. Model. Yuri Pevzner, Emilie Frugier, Vinushka Schalk, Amedeo Caflisch, H. Lee Woodcock III
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. PLoS Comput. Biol. 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
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. PLoS Comput. Biol. Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks
2014	J	`jnl`	Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. PLoS Comput. Biol. Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye
2013	J	`jnl`	How Does Catalase Release Nitric Oxide? A Computational Structure-Activity Relationship Study. J. Chem. Inf. Model. Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III
2012	J	`jnl`	Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors. J. Chem. Inf. Model. Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III
2012	J	`jnl`	Virtual Target Screening: Validation Using Kinase Inhibitors. J. Chem. Inf. Model. 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
2009	J	`jnl`	Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. J. Comput. Chem. Edina Rosta, H. Lee Woodcock III, Bernard R. Brooks, Gerhard Hummer
2009	J	`jnl`	CHARMM: The biomolecular simulation program. J. Comput. Chem. 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, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2008	J	`jnl`	CHARMMing: A New, Flexible Web Portal for CHARMM. J. Chem. Inf. Model. Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III
2007	J	`jnl`	Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J. Comput. Chem. H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks