Abstract
AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 A from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.
Publication types
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, P.H.S.
MeSH terms
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Azepines / chemistry
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Azepines / metabolism
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Bacterial Proteins / chemistry
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Bacterial Proteins / metabolism
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Benzamidines / chemistry
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Benzamidines / metabolism
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Biotin / chemistry
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Biotin / metabolism
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Camphor / chemistry
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Camphor / metabolism
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Camphor 5-Monooxygenase / chemistry
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Camphor 5-Monooxygenase / metabolism
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Cluster Analysis
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Computer Simulation
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Crystallography, X-Ray
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HIV Protease / chemistry
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HIV Protease / metabolism
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HIV Protease Inhibitors / chemistry
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HIV Protease Inhibitors / metabolism
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Hemagglutinins / chemistry
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Hemagglutinins / metabolism
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Immunoglobulin Fab Fragments / chemistry
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Immunoglobulin Fab Fragments / metabolism
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Ligands*
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Molecular Conformation*
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N-Acetylneuraminic Acid / chemistry
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N-Acetylneuraminic Acid / metabolism
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Phosphorylcholine / chemistry
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Phosphorylcholine / metabolism
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Protein Binding*
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Protein Conformation
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Software*
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Streptavidin
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Trypsin / chemistry
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Trypsin / metabolism
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User-Computer Interface
Substances
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Azepines
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Bacterial Proteins
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Benzamidines
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HIV Protease Inhibitors
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Hemagglutinins
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Immunoglobulin Fab Fragments
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Ligands
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XK 263
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Phosphorylcholine
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Biotin
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Camphor
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Streptavidin
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Camphor 5-Monooxygenase
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Trypsin
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HIV Protease
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N-Acetylneuraminic Acid
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benzamidine