Protein-Protein Docking Benchmark 2.0: an update.
Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z.
Boston University Bioinformatics Program, Boston, Massachusetts 02215, USA.
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.
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PMID: 15981264 [PubMed - indexed for MEDLINE]