Protein-protein docking benchmark version 4.0

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology

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Document Type



*Algorithms; Computational Biology; Crystallography, X-Ray; Databases, Protein; *Models, Chemical; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Interaction Mapping; Proteins; *Software


Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Systems Biology


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/.

DOI of Published Version



Proteins. 2010 Nov 15;78(15):3111-4. doi: 10.1002/prot.22830. Link to article on publisher's site

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