Protein-protein docking benchmark 2.0: An update

• Published in: Proteins, structure, function, and bioinformatics Vol. 60; no. 2; pp. 214 - 216
• Main Authors: Mintseris, Julian, Wiehe, Kevin, Pierce, Brian, Anderson, Robert, Chen, Rong, Janin, Joël, Weng, Zhiping
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.08.2005
• Subjects: Algorithms; Animals; Automation; complex structure; Computational Biology - methods; Computer Simulation; Crystallography, X-Ray; Databases, Protein; Dimerization; Humans; Internet; Macromolecular Substances; Models, Molecular; Models, Statistical; Molecular Conformation; Protein Binding; protein complexes; Protein Conformation; Protein Folding; Protein Interaction Mapping - methods; Protein Structure, Tertiary; protein-protein docking; protein-protein interactions; protein–protein interactions, complex structure; Proteomics - methods; Reproducibility of Results; Software; Structural Homology, Protein
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.20560

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.