Molecular Docking Screens Using Comparative Models of Proteins.
Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A, J Chem Inf Model, 2009 Oct 21 - link

Docking and chemoinformatic screens for new ligands and targets.
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK, Curr Opin Biotechnol, 2009 Aug - link

Automated docking screens: a feasibility study.
Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y, J Med Chem, 2009 Sep 24 - link

Docking for fragment inhibitors of AmpC beta-lactamase.
Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK, Proc Natl Acad Sci U S A, 2009 May 5 - link

Molecular docking and ligand specificity in fragment-based inhibitor discovery.
Chen Y, Shoichet BK, Nat Chem Biol, 2009 May - link

Exploiting ordered waters in molecular docking.
Huang N, Shoichet BK, J Med Chem, 2008 Aug 28 - link

Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK, J Med Chem, 2008 Apr 24 - link

Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK, J Mol Biol, 2008 Mar 28 - link

Benchmarking sets for molecular docking.
Huang N, Shoichet BK, Irwin JJ, J Med Chem, 2006 Nov 16 - link

Predicting substrates by docking high-energy intermediates to enzyme structures.
Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK, J Am Chem Soc, 2006 Dec 13 - link

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps.
Leach AR, Shoichet BK, Peishoff CE, J Med Chem, 2006 Oct 5 - link

Probing molecular docking in a charged model binding site.
Brenk R, Vetter SW, Boyce SE, Goodin DB, Shoichet BK, J Mol Biol, 2006 Apr 14 - link

Here be dragons: docking and screening in an uncharted region of chemical space.
Brenk R, Irwin JJ, Shoichet BK, J Biomol Screen, 2005 Oct - link

Hierarchical docking of databases of multiple ligand conformations.
Lorber DM, Shoichet BK, Curr Top Med Chem, 2005 - link

Decoys for docking.
Graves AP, Brenk R, Shoichet BK, J Med Chem, 2005 Jun 2 - link

Soft docking and multiple receptor conformations in virtual screening.
Ferrari AM, Wei BQ, Costantino L, Shoichet BK, J Med Chem, 2004 Oct 7 - link

Testing a flexible-receptor docking algorithm in a model binding site.
Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK, J Mol Biol, 2004 Apr 9 - link

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
McGovern SL, Shoichet BK, J Med Chem, 2003 Jul 3 - link

A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase.
Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS, J Biol Chem, 2003 Apr 18 - link

A model binding site for testing scoring functions in molecular docking.
Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK, J Mol Biol, 2002 Sep 13 - link

Lead discovery using molecular docking.
Shoichet BK, McGovern SL, Wei B, Irwin JJ, Curr Opin Chem Biol, 2002 Aug - link

Protein-protein docking with multiple residue conformations and residue substitutions.
Lorber DM, Udo MK, Shoichet BK, Protein Sci, 2002 Jun - link

Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.
Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK, J Med Chem, 2002 May 23 - link

Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation.
Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK, Proteins, 2001 Feb 1 - link

Ligand solvation in molecular docking.
Shoichet BK, Leach AR, Kuntz ID, Proteins, 1999 Jan 1 - link

Flexible ligand docking using conformational ensembles.
Lorber DM, Shoichet BK, Protein Sci, 1998 Apr - link

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.
Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN, Nat Struct Biol, 1996 Mar - link

Matching chemistry and shape in molecular docking.
Shoichet BK, Kuntz ID, Protein Eng, 1993 Sep - link

Protein docking and complementarity.
Shoichet BK, Kuntz ID, J Mol Biol, 1991 Sep 5 - link