Literature DB >> 19399780

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.

Garrett M Morris1, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson.   

Abstract

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. (c) 2009 Wiley Periodicals, Inc.

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Year:  2009        PMID： 19399780      PMCID： PMC2760638          DOI： 10.1002/jcc.21256

Source DB:  PubMed          Journal:  J Comput Chem        ISSN： 0192-8651            Impact factor:   3.376


  16 in total

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Journal:  Proteins       Date:  2002-06-01

Review 3.  Molecular recognition and docking algorithms.

Authors:  Natasja Brooijmans; Irwin D Kuntz
Journal:  Annu Rev Biophys Biomol Struct       Date:  2003-01-28

Review 4.  A review of protein-small molecule docking methods.

Authors:  R D Taylor; P J Jewsbury; J W Essex
Journal:  J Comput Aided Mol Des       Date:  2002-03       Impact factor: 3.686

Review 5.  Docking and scoring in virtual screening for drug discovery: methods and applications.

Authors:  Douglas B Kitchen; Hélène Decornez; John R Furr; Jürgen Bajorath
Journal:  Nat Rev Drug Discov       Date:  2004-11       Impact factor: 84.694

Review 6.  Docking: successes and challenges.

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7.  A component-based software environment for visualizing large macromolecular assemblies.

Authors:  Michel F Sanner
Journal:  Structure       Date:  2005-03       Impact factor: 5.006

8.  Automated docking of substrates to proteins by simulated annealing.

Authors:  D S Goodsell; A J Olson
Journal:  Proteins       Date:  1990

Review 9.  Automated docking of flexible ligands: applications of AutoDock.

Authors:  D S Goodsell; G M Morris; A J Olson
Journal:  J Mol Recognit       Date:  1996 Jan-Feb       Impact factor: 2.137

10.  Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4.

Authors:  G M Morris; D S Goodsell; R Huey; A J Olson
Journal:  J Comput Aided Mol Des       Date:  1996-08       Impact factor: 3.686
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