H. Lee Woodcock III

Publication Activity (10 Years)

Years Active: 2007-2022
Publications (10 Years): 6

Top Topics

Computational Chemistry

Protein Folding

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

J. Comput. Chem.

J. Comput. Aided Mol. Des.

Publications

Sai Lakshmana Vankayala, Luke C. Warrensford, Amanda R. Pittman, Benjamin C. Pollard, Fiona L. Kearns, Joseph D. Larkin, H. Lee Woodcock III
CIFDock: A novel CHARMM-based flexible receptor-flexible ligand docking protocol. J. Comput. Chem. 43 (2) (2022)
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
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J. Comput. Aided Mol. Des. 36 (4) (2022)
Fiona L. Kearns, Carrie Robart, M. Trent Kemp, Sai Lakshmana Vankayala, Brette M. Chapin, Eric V. Anslyn, H. Lee Woodcock III, Joseph D. Larkin
Modeling Boronic Acid Based Fluorescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid. J. Chem. Inf. Model. 59 (5) (2019)
Phillip S. Hudson, Kyungreem Han, H. Lee Woodcock III, Bernard R. Brooks
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. 32 (10) (2018)
Janez Konc, Benjamin T. Miller, Tanja Stular, Samo Lesnik, H. Lee Woodcock III, Bernard R. Brooks, Dusanka Janezic
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model. 55 (11) (2015)
Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock III, Bernard R. Brooks
Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. J. Comput. Chem. 36 (1) (2015)
Jacqueline C. Hargis, Justin K. White, Yu Chen, H. Lee Woodcock III
Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle? J. Chem. Inf. Model. 54 (5) (2014)
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
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial. PLoS Comput. Biol. 10 (7) (2014)
Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins. PLoS Comput. Biol. 10 (7) (2014)
Yuri Pevzner, Emilie Frugier, Vinushka Schalk, Amedeo Caflisch, H. Lee Woodcock III
Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. J. Chem. Inf. Model. 54 (9) (2014)
Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks
Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding. PLoS Comput. Biol. 10 (7) (2014)
Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III
How Does Catalase Release Nitric Oxide? A Computational Structure-Activity Relationship Study. J. Chem. Inf. Model. 53 (11) (2013)
Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III
Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors. J. Chem. Inf. Model. 52 (5) (2012)
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
Virtual Target Screening: Validation Using Kinase Inhibitors. J. Chem. Inf. Model. 52 (8) (2012)
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, V. 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
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Edina Rosta, H. Lee Woodcock III, Bernard R. Brooks, Gerhard Hummer
Artificial reaction coordinate "tunneling" in free-energy calculations: The catalytic reaction of RNase H. J. Comput. Chem. 30 (11) (2009)
Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodoscek, Bernard R. Brooks, H. Lee Woodcock III
CHARMMing: A New, Flexible Web Portal for CHARMM. J. Chem. Inf. Model. 48 (9) (2008)
H. Lee Woodcock III, Milan Hodoscek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer III, Bernard R. Brooks
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. J. Comput. Chem. 28 (9) (2007)