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

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Proteins, ISSN: 1097-0134, Vol: 78, Issue: 15, Page: 3104-10

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Hwang, Howook; Vreven, Thom; Pierce, Brian G.; Hung, Jui-Hung; Weng, Zhiping
Biochemistry, Genetics and Molecular Biology; *Algorithms; Animals; Cattle; Cluster Analysis; Computational Biology; Hordeum; Protein Binding; Protein Interaction Mapping; Proteins; Software; Bioinformatics; Computational Biology; Systems Biology
article description
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.