The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI

Proteins. 2007 Dec 1;69(4):719-25. doi: 10.1002/prot.21747.

Abstract

We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium-accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium-accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial-stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Cluster Analysis
  • Computational Biology / methods*
  • Computer Simulation*
  • Crystallography, X-Ray / methods
  • Databases, Protein
  • Dimerization
  • Genomics
  • Ligands
  • Molecular Conformation
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping*
  • Proteins / chemistry*
  • Proteomics / methods*
  • Software

Substances

  • Ligands
  • Proteins