DOCK 6: Impact of New Features and Current Docking Performance

被引:510
作者
Allen, William J. [1 ]
Balius, Trent E. [1 ]
Mukherjee, Sudipto [1 ]
Brozell, Scott R. [2 ,3 ]
Moustakas, Demetri T. [4 ]
Lang, P. Therese [5 ]
Case, David A. [2 ,3 ]
Kuntz, Irwin D. [6 ]
Rizzo, Robert C. [1 ,7 ,8 ]
机构
[1] SUNY Stony Brook, Dept Appl Math & Stat, Stony Brook, NY 11794 USA
[2] Rutgers State Univ, BioMaPs Inst, Piscataway, NJ 08854 USA
[3] Rutgers State Univ, Dept Chem & Chem Biol, Piscataway, NJ 08854 USA
[4] R&D Boston, AstraZeneca, Infect Innovat Med Unit, Waltham, MA 02451 USA
[5] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA
[6] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA
[7] SUNY Stony Brook, Inst Chem Biol & Drug Discovery, Stony Brook, NY 11794 USA
[8] SUNY Stony Brook, Laufer Ctr Phys & Quantitat Biol, Stony Brook, NY 11794 USA
基金
美国国家卫生研究院;
关键词
docking; pose reproduction; cross-docking; enrichment; virtual screening; ligand flexibility; DOCK; REVERSE-TRANSCRIPTASE INHIBITOR; MULTIPLE RECEPTOR CONFORMATIONS; AUTOMATED MOLECULAR DOCKING; LIGAND-BINDING; HYDROPHOBIC ENCLOSURE; EFFICIENT GENERATION; PROTEIN FLEXIBILITY; STRUCTURAL-ANALYSIS; CRYSTAL-STRUCTURES; ACCURATE DOCKING;
D O I
10.1002/jcc.23905
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) 5.4 (65.2%) 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% 13.6% 9.1% and scoring 24.4% 21.1% 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at . (c) 2015 Wiley Periodicals, Inc.
引用
收藏
页码:1132 / 1156
页数:25
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