Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

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TitlePerformance of ZDOCK and ZRANK in CAPRI rounds 13-19.
Publication TypeJournal Article
Year of Publication2010
AuthorsHwang, H, Vreven, T, Pierce, BG, Hung, J-H, Weng, Z
JournalProteins
Volume78
Issue15
Pagination3104-10
Date Published2010 Nov 15
ISSN1097-0134
KeywordsAlgorithms, Animals, Cattle, Cluster Analysis, Computational Biology, Hordeum, Protein Binding, Protein Interaction Mapping, Proteins, Software
Abstract

We report the performance of the ZDOCK and ZRANK algorithms in CAPRI rounds 13-19 and introduce a novel measure atom contact frequency (ACF). To compute ACF, we identify the residues that most often make contact with the binding partner in the complete set of ZDOCK predictions for each target. We used ACF to predict the interface of the proteins, which, in combination with the biological data available in the literature, is a valuable addition to our docking pipeline. Furthermore, we incorporated a straightforward and efficient clustering algorithm with two purposes: (1) to determine clusters of similar docking poses (corresponding to energy funnels) and (2) to remove redundancies from the final set of predictions. With these new developments, we achieved at least one acceptable prediction for targets 29 and 36, at least one medium-quality prediction for targets 41 and 42, and at least one high-quality prediction for targets 37 and 40; thus, we succeeded for six out of a total of 12 targets.

DOI10.1002/prot.22764
Alternate JournalProteins
PubMed ID20936681
PubMed Central IDPMC3936321
Grant ListR01 GM084884 / GM / NIGMS NIH HHS / United States
R01 GM084884 / GM / NIGMS NIH HHS / United States