Research Article

ZRANK: Reranking protein docking predictions with an optimized energy function

  1. Brian Pierce,
  2. Zhiping Weng*

Article first published online: 20 MAR 2007

DOI: 10.1002/prot.21373

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 67, Issue 4, pages 1078–1086, June 2007

Additional Information

How to Cite

Pierce, B. and Weng, Z. (2007), ZRANK: Reranking protein docking predictions with an optimized energy function. Proteins: Structure, Function, and Bioinformatics, 67: 1078–1086. doi: 10.1002/prot.21373

Author Information

  1. Bioinformatics Program, Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215

*Bioinformatics Program, Department of Biomedical Engineering, Boston University, Boston, MA 02215

Publication History

  1. Issue published online: 1 MAY 2007
  2. Article first published online: 20 MAR 2007
  3. Manuscript Accepted: 13 DEC 2006
  4. Manuscript Revised: 28 OCT 2006
  5. Manuscript Received: 10 JUN 2006

Funded by

  • NSF. Grant Numbers: DBI-0078194, DBI-0133834, DBI-0116574

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Keywords:

  • protein docking;
  • rigid body docking;
  • reranking;
  • refinement

Abstract

Protein–protein docking requires fast and effective methods to quickly discriminate correct from incorrect predictions generated by initial-stage docking. We have developed and tested a scoring function that utilizes detailed electrostatics, van der Waals, and desolvation to rescore initial-stage docking predictions. Weights for the scoring terms were optimized for a set of test cases, and this optimized function was then tested on an independent set of nonredundant cases. This program, named ZRANK, is shown to significantly improve the success rate over the initial ZDOCK rankings across a large benchmark. The amount of test cases with No. 1 ranked hits increased from 2 to 11 and from 6 to 12 when predictions from two ZDOCK versions were considered. ZRANK can be applied either as a refinement protocol in itself or as a preprocessing stage to enrich the well-ranked hits prior to further refinement. Proteins 2007. © 2007 Wiley-Liss, Inc.

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