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Keywords:

  • protein docking;
  • protein–protein docking;
  • benchmark;
  • enzyme-inhibitor complexes;
  • antibody-antigen complexes

Abstract

We have developed a nonredundant benchmark for testing protein–protein docking algorithms. Currently it contains 59 test cases: 22 enzyme-inhibitor complexes, 19 antibody-antigen complexes, 11 other complexes, and 7 difficult test cases. Thirty-one of the test cases, for which the unbound structures of both the receptor and ligand are available, are classified as follows: 16 enzyme-inhibitor, 5 antibody-antigen, 5 others, and 5 difficult. Such a centralized resource should benefit the docking community not only as a large curated test set but also as a common ground for comparing different algorithms. The benchmark is available at (http://zlab.bu.edu/∼rong/dock/benchmark.shtml). Proteins 2003;52:88–91. © 2003 Wiley-Liss, Inc.