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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Author(s) -
Morris Garrett M.,
Huey Ruth,
Lindstrom William,
Sanner Michel F.,
Belew Richard K.,
Goodsell David S.,
Olson Arthur J.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21256
Subject(s) - docking (animal) , searching the conformational space for docking , chemistry , protein–ligand docking , computer science , grid , flexibility (engineering) , covalent bond , graphical user interface , combinatorial chemistry , computational biology , virtual screening , molecular dynamics , binding site , computational chemistry , biochemistry , mathematics , biology , organic chemistry , programming language , medicine , statistics , nursing , geometry
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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
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