Title

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology

Date

11-15-2010

Document Type

Article

Medical Subject Headings

*Algorithms; Animals; Cattle; Cluster Analysis; Computational Biology; Hordeum; Protein Binding; Protein Interaction Mapping; Proteins; Software

Disciplines

Bioinformatics | Computational Biology | Systems Biology

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.

Rights and Permissions

Citation: Proteins. 2010 Nov 15;78(15):3104-10. doi: 10.1002/prot.22764. Link to article on publisher's site

Related Resources

Link to Article in PubMed