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Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82


Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801.

DOCK Blaster

Huang, Shoichet and Irwin, J. Med. Chem., 2006, 49(23), 6789-6801 (for now). Will be published in 2008.


Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC. J Comput Aided Mol Des. 2006 Oct-Nov;20(10-11):601-19

Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. RNA. 2009 Jun;15(6):1219-30

Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. J Comput Chem. 2015 Jun 5;36(15):1132-56

DOCK 3.5.54

Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 5 (8), 739-49 (2005).

Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Science 7, 938-950 (1998).

Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK. A model binding site for testing scoring functions in molecular docking. J Mol Biol 322, 339-55 (2002).

Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).


Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007).


Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ and Shoichet BK, Predicting substrates by docking high-energy intermediates to enzyme substuctures. J Am Chem Soc. 128, 15882-91 (2006).