Primary references for AutoDock, and some published applications of AutoDock.
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 2009, 16: 2785-91.
AutoDock 3 & 4
Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function J. Computational Chemistry, 19: 1639-1662.
AutoDock 4 Scoring Function
Huey, R., Morris, G. M., Olson, A. J. and Goodsell, D. S. (2007), A Semiempirical Free Energy Force Field with Charge-Based Desolvation J. Computational Chemistry, 28: 1145-1152.
Morris, G. M., Goodsell, D. S., Huey, R. and Olson, A. J. (1996), Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 J. Computer-Aided Molecular Design, 10: 293-304.
Goodsell, D. S. and Olson, A. J. (1990), Automated Docking of Substrates to Proteins by Simulated Annealing Proteins:Structure, Function and Genetics., 8: 195-202.
Reviews of Applications
Goodsell, D. S., Morris, G. M. and Olson, A. J. (1996), Automated Docking of Flexible Ligands: Applications of AutoDock J. Mol. Recognition, 9: 1-5.
Selected Applications and Citations of AutoDock
Sotriffer, C.A., Flader, W., Winger, R.H., Rode, B.M., Liedl, K.R., and Varga, J.M. (2000), "Automated docking of ligands to antibodies: methods and applications" Methods: A Companion to Methods in Enzymology, 20: 280-291.
Minke, W.E., Diller, D.J., Hol, W.G., and Verlinde C. L. (1999), "The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case" J. Med. Chem., 42: 1778-1788.
Laederach, A., Dowd, M.K., Coutinho, P.M., and Reilly, P.J. (1999), "Automated Docking of Maltose, 2-Deoxymaltose, and Maltotetraose into the Soybean beta-Amylase Active Site", Proteins:Structure, Function and Genetics, 37: 166-175.
Matias, P. M., Saraiva, L. M., Soares, C. M., Coelho, A. V., LeGall, J., and Armenia Carrondo, M. (1999), "Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774: primary sequence determination, crystallographic refinement at 1.8 Å and modelling studies of its interaction with the tetrahaem cytochrome c3", JBIC, 4: 478-494.
Bitomsky, W. and Wade, R. C. (1999), "Docking of Glycosaminoglycans to Heparin-Binding Proteins: Validation for aFGF, bFGF, and Antithrombin and Application to IL-8", J. Am. Chem. Soc., 121: 3004-3013.
Lorber, D. M. (1999), "Computational drug design", Chemistry & Biology, 6: R227-R228.
Rao, M. S. and Olson, A. J. (1999), "Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach", Proteins, 34: 173-83.
Walters, W.P., Stahl, M.T., and Murcko, M.A. (1998), "Virtual screening-an overview", Drug Discovery Today, 3: 160-178.
Heine, A., Stura, E.A., Yli-Kauhaluoma, J.T., Gao, C., Deng, Q., Beno, B.R., Houk, K.N., Janda, K.D., and Wilson, I.A. (1998), "An antibody exo Diels-Alderase inhibitor complex at 1.95 Å resolution", Science, 279: 1934-1940.
Coutinho, P. M., Dowd, M. K., and Reilly, P. J., (1998), "Automated Docking of -(1,4)- and -(1,6)-Linked Glucosyl Trisaccharides in the Glucoamylase Active Site", Industrial & Engineering Chemistry Research, 37: 2148-2157. [Abstract - requires subscription to ACS.org].
Lozano, J. J., López-de-Briñas, E., Centeno, N.B., Guigó, R. and Sanz, F.(1997), "Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ", J. Computer-Aided Molecular Design, 11: 395-408.
Mahmoudian, M. (1997), "The cannabinoid receptor: Computer-aided molecular modeling and docking of ligand", J. Molecular Graphics & Modelling, 15: 149-153.
Coutinho, P. M., Dowd, M. K. and Reilly, P. J. (1997), "Automated Docking of Glucosyl Disaccharides in the Glucoamylase Active Site", Proteins: Str. Func. and Genet., 28: 162-173.
Coutinho, P. M., Dowd, M. K. and Reilly, P. J. (1997), "Automated Docking of Monosaccharide Substrates and Analogues and Melthyl alpha-Acarviosinide in the Glucoamylase Active Site", Proteins: Str. Func. and Genet., 27: 235-248.
Neurath, A. R., Jiang, S., Strick, K. L., Li, Y.-Y., and Debnath, A. K. (1996), "Bovine beta-lactoglobulin modified by 3-hydroxyphthalic anhydride blocks the CD4 cell receptor for HIV", Nature Medicine, 2: 230-234.
Gamper, A.M., Winger, R.H., Liedl, K.R., Sotriffer, C.A., Varga, J.M., Kroemer, R.T., and Rode, B.M. (1996), "Comparative molecular field analysis of haptens docked to the multispecific antibody IgE", J. Med. Chem., 39: 3882-3888.
Sotriffer, C. A., Liedl, K. R., Winger, R. H., Gamper, A. M., Kroemer, R. T., Linthicum, D. S., Rode, B.-M. and Varga, J. M. (1996) "Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking", Molecular Immunology, 33: 129-144.
Zhang, T. and Koshland, D. E. (1995 ), "Modeling substrate binding in Thermus thermophilus isopropylmalate dehydrogenase", Protein Science, 4: 84-92.
Kedishvili, N. Y., Bosron, W. F., Stone, C. L., Hurley, T.D., Peggs, C. F., Thomasson, H. R., Popov, K. M., Carr, L. G., Edenberg, H. J. and Li, T.-K. (1995), "Expression and kinetic characterization of recombinant human stomach alcohol dehydrogenase", J. Biol. Chem., 270: 3625-3630.
Stone, C. L., Hurley, T. D., Peggs, C. F., Kedishvili, N. Y., Davis, G. J., Thomasson, H. R., Li, T.-K. and Bosron, W. F. (1995), "Cimetidine inhibition of human gastric and liver alcohol dehydrogenase isoenzymes: identification of inhibitor complexes by kinetic and molecular modeling", Biochemistry, 34: 4008-4014.
Tummino, P. J., Ferguson, D., Jacobs, C. M ., Tait, B., Hupe, L., Lunney, E. and Hupe, D. (1995), "Competitive inhibition of HIV-1 protease by biphenyl carboxylic acids", Arch. Biochem. Biophys., 316: 523-528.
Friedman, A. R., Roberts, V. A. and Tainer, J. A. (1994) "Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes", Proteins: Str. Func. and Genet., 20: 15-24.
Lunney, E. A., Hagen, S. E., Domagala, J. M., Humblet, C., Kosinski, J., Tait, B. D., Warmus, J. S., Wilson, M., F erguson, D., Hupe, D., Tummino, P. J., Baldwin, E. T., Bhat, T. N., Liu, B. and Erickson, J. W. (1994), "A novel nonpeptide HIV-1 protease inhibitor: elucidation of the binding modes and its application in the design of related analogs", J. Med. Chem., 37 : 2664-2677.
Vara Prasad, J. V. N., Para, K.S., Ortwine, D. F., Dunbar, Jr., J. B., Ferguson, D., Tummino, P. J., Hupe, D., Tait, B. D., Domagala, J. M., Humblet, C., Bhat, T. N., Liu, B., Guerin, D. M. A., Baldwin, E. T., Erickson, J. W. and Sawyer, T. K. (1994), "Novel series of achiral, low molecular weight, and potent HIV-1 protease inhibitors", J. Am. Chem. Soc., 116: 6989-6990.
Stoddard, B. L. and Koshland, Jr., D. E. (1993), "Molecular recognition analyzed by docking simulations: The aspartate receptor and isocitrate dehydrogenase from Escherichia coli", Proc. Natl. Acad. Sci. USA, 90: 1146-1153.
Jeffery, C. J. and Koshland, Jr., D. E. (1993), "Three-dimensional structural model of the serine receptor ligand binding domain", Protein Science, 2: 559-566.
Goodsell, D. S., Lauble, H., Stout, C. D. and Olson, A. J. (1993), "Automated Docking in Crystallography: Analysis of the Substrates of Aconitase", Proteins: Str. Func. and Genet., 17: 1-10.
Stoddard, B.L. and Koshland, Jr., D.E. (1992), "Prediction of a receptor protein complex using a binary docking method", Nature, 358: 774-776.
Lunney, E. (1995) Network Science, 1: http://www.netsci.org/Science/Cheminform/feature01.html. Structure-Based Design and Two Aspartic Proteases