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AutoDock References

Primary References

AutoDock 3.0
    Morris, G. M.,  Goodsell, D. S.,  Halliday, R.S.,  Huey, R.,  Hart, W. E.,  Belew, R. K.  and  Olson, A. J.  (1998), J. Computational Chemistry, 19: 1639-1662.
    "Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function".
    (Abstract).
    AutoDock 2.4
    Morris, G. M.,  Goodsell, D. S.,  Huey, R.  and  Olson, A. J.  (1996), J. Computer-Aided Molecular Design, 10: 293-304.
    "Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4".
    (Abstract).
    AutoDock 1.0
    Goodsell, D. S.  and  Olson, A. J. (1990), Proteins: Str. Func. and Genet., 8: 195-202.
    "Automated Docking of Substrates to Proteins by Simulated Annealing".

Reviews of Applications

  1. Goodsell, D. S.,  Morris, G. M.  and  Olson, A. J. (1996), J. Mol. Recognition, 9: 1-5.

    2. "Docking of Flexible Ligands: Applications of AutoDock".
    (Abstract).


Selected Applications and Citations of AutoDock

  1. Sotriffer, C.A.,  Flader, W.,  Winger, R.H.,  Rode, B.M.,  Liedl, K.R.,  and  Varga, J.M. (2000), Methods: A Companion to Methods in Enzymology, 20: 280-291

    2. "Automated docking of ligands to antibodies: methods and applications".
    [Abstract], [Full text].
     
  2. Minke, W.E.,  Diller, D.J.,  Hol, W.G.,  and  Verlinde C. L. (1999), J. Med. Chem., 42: 1778-1788.

    3. "The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case".
    [Abstract], [Full text].
     
  3. Laederach, A.,  Dowd, M.K.,  Coutinho, P.M.,  and  Reilly, P.J. (1999), Proteins:Structure, Function and Genetics, 37: 166-175.

    4. "Automated Docking of Maltose, 2-Deoxymaltose, and Maltotetraose into the Soybean beta-Amylase Active Site".
     
  4. Matias, P. M.,  Saraiva, L. M.,  Soares, C. M.,  Coelho, A. V.,  LeGall, J.,  and  Armenia Carrondo, M. (1999) JBIC, 4: 478-494.

    5. "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".
     
  5. Bitomsky, W.  and  Wade, R. C. (1999), J. Am. Chem. Soc., 121: 3004-3013.

    6. "Docking of Glycosaminoglycans to Heparin-Binding Proteins: Validation for aFGF, bFGF, and Antithrombin and Application to IL-8".
     
  6. Lorber, D. M. (1999), Chemistry & Biology, 6: R227-R228.

    7. "Computational drug design".
    [Abstract], [Full text].
     
  7. Rao, M. S.  and  Olson, A. J. (1999), Proteins, 34: 173-83.

    8. "Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach".
     
  8. Walters, W.P.,  Stahl, M.T.,  and  Murcko, M.A. (1998),  Drug Discovery Today, 3: 160-178.

    9. "Virtual screening-an overview".
     
  9. 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), Science, 279: 1934-1940.

    10. "An antibody exo Diels-Alderase inhibitor complex at 1.95 Å resolution".
     
  10. Coutinho, P. M.,  Dowd, M. K.,  and  Reilly, P. J., (1998), Industrial & Engineering Chemistry Research, 37: 2148-2157.

    11. "Automated Docking of -(1,4)- and -(1,6)-Linked Glucosyl Trisaccharides in the Glucoamylase Active Site".
     (Abstract - requires subscription to ACS.org).
     
  11. Lozano, J. J.,  López-de-Briñas, E.,  Centeno, N.B.,  Guigó, R.  and  Sanz, F.(1997), J. Computer-Aided Molecular Design, 11:  395-408.

    12. "Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ".
    (Abstract).
     
  12. Mahmoudian, M. (1997), J. Molecular Graphics & Modelling, 15: 149-153.

    13. "The cannabinoid receptor: Computer-aided molecular modeling and docking of ligand".
    (Abstract).
     
  13. Coutinho, P. M.,  Dowd, M. K.  and  Reilly, P. J. (1997), Proteins: Str. Func. and Genet., 28: 162-173.

    14. "Automated Docking of Glucosyl Disaccharides in the Glucoamylase Active Site".
    (Abstract).
     
  14. Coutinho, P. M.,  Dowd, M. K.  and  Reilly, P. J. (1997), Proteins: Str. Func. and Genet., 27: 235-248.

    15. "Automated Docking of Monosaccharide Substrates and Analogues and Melthyl alpha-Acarviosinide in the Glucoamylase Active Site".
    (Abstract).
     
  15. Neurath, A. R.,  Jiang, S.,  Strick, K. L.,  Li, Y.-Y.,  and  Debnath, A. K. (1996), Nature Medicine, 2: 230-234.

    16. "Bovine beta-lactoglobulin modified by 3-hydroxyphthalic anhydride blocks the CD4 cell receptor for HIV".
     
  16. Gamper, A.M.,   Winger, R.H.,  Liedl, K.R.,  Sotriffer, C.A.,  Varga, J.M.,  Kroemer, R.T.,  and  Rode, B.M. (1996), J. Med. Chem., 39: 3882-3888.

    17. "Comparative molecular field analysis of haptens docked to the multispecific antibody IgE".
    (Abstract).
     
  17. 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) Molecular Immunology, 33: 129-144.

    18. "Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking".
    (Abstract).
     
  18. Zhang, T.  and  Koshland, D. E. (1995 ), Protein Science, 4: 84-92.

    19. "Modeling substrate binding in Thermus thermophilus isopropylmalate dehydrogenase".
    (Abstract).
     
  19. 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) J. Biol. Chem., 270: 3625-3630.

    20. "Expression and kinetic characterization of recombinant human stomach alcohol dehydrogenase".
    (Abstract).
     
  20. 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) Biochemistry, 34: 4008-4014.

    21. "Cimetidine inhibition of human gastric and liver alcohol dehydrogenase isoenzymes: identification of inhibitor complexes by kinetic and molecular modeling".
    (Abstract).
     
  21. Tummino, P. J.,  Ferguson, D.,  Jacobs, C. M .,  Tait, B.,  Hupe, L.,  Lunney, E.  and  Hupe, D. (1995) Arch. Biochem. Biophys., 316: 523-528.

    22. "Competitive inhibition of HIV-1 protease by biphenyl carboxylic acids".
    (Abstract).
     
  22. Friedman, A. R.,  Roberts, V. A.   and  Tainer, J. A. (1994) Proteins: Str. Func. and Genet., 20: 15-24.

    23. "Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes".
    (Abstract).
     
  23. 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) J. Med. Chem., 37 : 2664-2677.

    24. "A novel nonpeptide HIV-1 protease inhibitor: elucidation of the binding modes and its application in the design of related analogs".
    (Abstract).
     
  24. 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) J. Am. Chem. Soc., 116: 6989-6990.

    25. "Novel series of achiral, low molecular weight, and potent HIV-1 protease inhibitors".
    (Abstract).
     
  25. Stoddard, B. L.  and  Koshland, Jr., D. E. (1993) Proc. Natl. Acad. Sci. USA 90: 1146-1153.

    26. "Molecular recognition analyzed by docking simulations: The aspartate receptor and isocitrate dehydrogenase from Escherichia coli".
    (Abstract).
     
  26. Jeffery, C. J.  and  Koshland, Jr., D. E. (1993) Protein Science 2: 559-566.

    27. "Three-dimensional structural model of the serine receptor ligand binding domain".
    (Abstract).
     
  27. Goodsell, D. S.,  Lauble, H.,  Stout, C. D.  and  Olson, A. J. (1993) Proteins: Str. Func. and Genet., 17: 1-10.

    28. "Automated Docking in Crystallography: Analysis of the Substrates of Aconitase".
    (Abstract).
     
  28. Stoddard, B.L.  and  Koshland, Jr., D.E. (1992) Nature, 358: 774-776.

    29. "Prediction of a receptor protein complex using a binary docking method".
     (Abstract).

 

Web publications

  1. Lunney, E. (1995) Network Science, 1: http://www.netsci.org/Science/Cheminform/feature01.html.

    2. "Structure-Based Design and Two Aspartic Proteases".
    Article.
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