Protein–protein docking benchmark version 4.0

We updated our protein–protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high‐resolution complex structures that are nonredundant at the family–family pair level, for which the X‐ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound–unbound cases that can be used for protein–protein docking method development and assessment. Seventeen of the newly added cases are enzyme‐inhibitor complexes, and we found no new antigen‐antibody complexes. Classifying the new cases according to expected difficulty for protein–protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/ Proteins 2010. © 2010 Wiley‐Liss, Inc.

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