title: A protein-protein docking benchmark.
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).
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Rong
authors.initials: R
authors.lastname: Chen
authors.forename: Julian
authors.initials: J
authors.lastname: Mintseris
authors.forename: Joël
authors.initials: J
authors.lastname: Janin
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D000941:Antigens / Q000737:chemistry / Q000276:immunology; D001665:Binding Sites; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances; D008958:Models, Molecular; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D000906:Antibodies; D000941:Antigens; D004791:Enzyme Inhibitors; D004798:Enzymes; D046911:Macromolecular Substances; D011506:Proteins