Research Article

Protein–protein docking benchmark 2.0: An update

  1. Julian Mintseris1,
  2. Kevin Wiehe1,
  3. Brian Pierce1,
  4. Robert Anderson1,
  5. Rong Chen1,
  6. Joël Janin2,
  7. Zhiping Weng1,3,*

Article first published online: 24 JUN 2005

DOI: 10.1002/prot.20560

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Special Issue: Second Meeting on the Critical Assessment of PRedicted Interactions

Volume 60, Issue 2, pages 214–216, 1 August 2005

Additional Information

How to Cite

Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J. and Weng, Z. (2005), Protein–protein docking benchmark 2.0: An update. Proteins: Structure, Function, and Bioinformatics, 60: 214–216. doi: 10.1002/prot.20560

Author Information

  1. 1

    Boston University Bioinformatics Program, Boston, Massachusetts

  2. 2

    Laboratoire d'Enzymologie et Biochimie Structurales, Gif-sur-Yvette, France

  3. 3

    Boston University Biomedical Engineering Department, Boston, Massachusetts

*Department of Biomedical Engineering and Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215

Publication History

  1. Issue published online: 24 JUN 2005
  2. Article first published online: 24 JUN 2005
  3. Manuscript Accepted: 21 FEB 2005
  4. Manuscript Received: 21 JAN 2005

Funded by

  • U.S. Department of Energy Computational Science Graduate Fellowship
  • National Science Foundation. Grant Numbers: DBI-0078194, DBI-0133834, DBI-0116574

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Keywords:

  • protein–protein docking;
  • protein complexes;
  • protein–protein interactions, complex structure

Abstract

We present a new version of the Protein–Protein Docking Benchmark, reconstructed from the bottom up to include more complexes, particularly focusing on more unbound–unbound test cases. SCOP (Structural Classification of Proteins) was used to assess redundancy between the complexes in this version. The new benchmark consists of 72 unbound–unbound cases, with 52 rigid-body cases, 13 medium-difficulty cases, and 7 high-difficulty cases with substantial conformational change. In addition, we retained 12 antibody–antigen test cases with the antibody structure in the bound form. The new benchmark provides a platform for evaluating the progress of docking methods on a wide variety of targets. The new version of the benchmark is available to the public at http://zlab.bu.edu/benchmark2. Proteins 2005;60:214–216. © 2005 Wiley-Liss, Inc.

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