Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

UMMS Affiliation

Program in Bioinformatics and Integrative Biology

Publication Date


Document Type



Algorithms; Animals; Humans; *Molecular Docking Simulation; Polynucleotide Adenylyltransferase; Protein Binding; Protein Conformation; Protein Interaction Mapping; Proteins; Software; Thermodynamics; Vaccinia virus; Viral Proteins


Bioinformatics | Computational Biology | Molecular Biology | Structural Biology


We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein-protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall and r=0.72 for the rigid complexes.


antibody–antigen, binding free energy, conformational change, protein–protein complex structure, protein–protein interface

DOI of Published Version



J Mol Biol. 2015 Sep 25;427(19):3031-41. doi: 10.1016/j.jmb.2015.07.016. Epub 2015 Jul 29. Link to article on publisher's site

Journal/Book/Conference Title

Journal of molecular biology

Related Resources

Link to Article in PubMed

PubMed ID