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High throughput docking for library design and library prioritization
Author(s) -
Diller David J.,
Merz Kenneth M.
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/1097-0134(20010501)43:2<113::aid-prot1023>3.0.co;2-t
Subject(s) - prioritization , docking (animal) , computational biology , computer science , protein data bank , chemistry , protein–ligand docking , combinatorial chemistry , drug discovery , protein structure , biology , biochemistry , virtual screening , engineering , medicine , nursing , management science
The prioritization of the screening of combinatorial libraries is an extremely important task for the rapid identification of tight binding ligands and ultimately pharmaceutical compounds. When structural information for the target is available, molecular docking is an approach that can be used for prioritization. Here, we present the initial validation of a new rapid approach to molecular docking developed for prioritizing combinatorial libraries. The algorithm is tested on 103 individual cases from the protein data bank and in nearly 90% of these cases docks the ligand to within 2.0 Å of the observed binding mode. Because the mean CPU time is <5 s/mol, this approach can process hundreds of thousands of compounds per week. Furthermore, if a somewhat less thorough search is performed, the search time drops to 1 s/mol, thus allowing millions of compounds to be docked per week and tested for potential activity. Proteins 2001;43:113–124. © 2001 Wiley‐Liss, Inc.