Proteinprotein docking benchmark version 4.0

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICSProtein–proteindockingbenchmarkversion4.01 1 2 1*Howook Hwang, Thom Vreven, Joe¨l Janin, and Zhiping Weng1Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester,Massachusetts 016052Yeast Structural Genomics, IBBMC Universite´ Paris-Sud, CNRS UMR 8619, 91405-Orsay, FranceINTRODUCTIONABSTRACTDuring the last decade, the computational protein–protein docking field hasWe updated our protein–proteinadvanced considerably. In part, this is due to the efforts of making algorithmsdocking benchmark to include 1–8available to the community through web servers and/or downloadable packages,complexes that became available 9the community-wide CAPRI experiment, and the development of publically avail-since our previous release. As 10,11able benchmarks of protein–protein complexes.before, we only considered high-A protein–protein docking benchmark provides the community with a set ofresolution complex structures thatnon-redundant protein–protein complexes for which the complex structure andare nonredundant at the family–the constituent unbound structures are available. A benchmark forms a subset offamily pair level, for which the12X-ray or NMR unbound struc- the Protein Data Bank (PDB) and provides a standard dataset that can be usedtures of the constituent proteins for systematic comparison of docking algorithms. Quantity and diversity of inter-are also available. Benchmark ...