Development and validation of a modular, extensible docking program: DOCK 5.
Moustakas DT, Lang PT, Pegg S, Pettersen E, Kuntz ID, Brooijmans N, Rizzo RC, J Comput Aided Mol Des, 2006 Oct-Nov - link

Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA.
Wang J, Kang X, Kuntz ID, Kollman PA, J Med Chem, 2005 Apr 7 - link

Molecular recognition and docking algorithms.
Brooijmans N, Kuntz ID, Annu Rev Biophys Biomol Struct, 2003 - link

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases.
Ewing TJ, Makino S, Skillman AG, Kuntz ID, J Comput Aided Mol Des, 2001 May - link

Design, docking, and evaluation of multiple libraries against multiple targets.
Lamb ML, Burdick KW, Toba S, Young MM, Skillman AG, Zou X, Arnold JR, Kuntz ID, Proteins, 2001 Feb 15 - link

DREAM++: flexible docking program for virtual combinatorial libraries.
Makino S, Ewing TJ, Kuntz ID, J Comput Aided Mol Des, 1999 Sep - link

Flexible ligand docking: a multistep strategy approach.
Wang J, Kollman PA, Kuntz ID, Proteins, 1999 Jul 1 - link

Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.
Hendrix DK, Klein TE, Kuntz ID, Protein Sci, 1999 May - link

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

CombiDOCK: structure-based combinatorial docking and library design.
Sun Y, Ewing TJ, Skillman AG, Kuntz ID, J Comput Aided Mol Des, 1998 Nov - link

Surface solid angle-based site points for molecular docking.
Hendrix DK, Kuntz ID, Pac Symp Biocomput, 1998 - link

Characterization of receptors with a new negative image: use in molecular docking and lead optimization.
Oshiro CM, Kuntz ID, Proteins, 1998 Feb 15 - link

Molecular docking to ensembles of protein structures.
Knegtel RM, Kuntz ID, Oshiro CM, J Mol Biol, 1997 Feb 21 - link

Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal.
Gschwend DA, Kuntz ID, J Comput Aided Mol Des, 1996 Apr - link

Molecular docking towards drug discovery.
Gschwend DA, Good AC, Kuntz ID, J Mol Recognit, 1996 Mar-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

Flexible ligand docking using a genetic algorithm.
Oshiro CM, Kuntz ID, Dixon JS, J Comput Aided Mol Des, 1995 Apr - link

Docking analysis of a series of benzylamino acetylcholinesterase inhibitors with a phthalimide, benzoyl, or indanone moiety.
Yamamoto Y, Ishihara Y, Kuntz ID, J Med Chem, 1994 Sep 16 - link

Orientational sampling and rigid-body minimization in molecular docking.
Meng EC, Gschwend DA, Blaney JM, Kuntz ID, Proteins, 1993 Nov - 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

A new approach to the problem of docking two molecules: the ellipsoid algorithm.
Billeter M, Havel TF, Kuntz ID, Biopolymers, 1987 Jun - link

Docking flexible ligands to macromolecular receptors by molecular shape.
DesJarlais RL, Sheridan RP, Dixon JS, Kuntz ID, Venkataraghavan R, J Med Chem, 1986 Nov - link