Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Proteins. 2010 Nov 15;78(15):3104-10. doi: 10.1002/prot.22764.

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

Author information

  • 1Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.

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.

© 2010 Wiley-Liss, Inc.

PMID:
20936681
[PubMed - indexed for MEDLINE]
PMCID:
PMC3936321
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for John Wiley & Sons, Inc. Icon for PubMed Central
    Loading ...
    Write to the Help Desk