Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 52, Issue 1, Pages 107-112Publisher
WILEY
DOI: 10.1002/prot.10397
Keywords
CAPRI; unbound docking; flexible docking; PatchDock; binding site focusing
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Funding
- NCI NIH HHS [N01-CO-12400] Funding Source: Medline
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We present a very efficient rigid unbound soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the correct solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience. (C) 2003 Wiley-Liss, Inc.
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