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A protein–protein docking benchmark
Author(s) -
Chen Rong,
Mintseris Julian,
Janin Joël,
Weng Zhiping
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10390
Subject(s) - docking (animal) , benchmark (surveying) , dock , computational biology , computer science , macromolecular docking , biochemistry , protein structure , biology , medicine , geography , geodesy , nursing
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).