title: Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
abstract: 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.
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Thom
authors.initials: T
authors.lastname: Vreven
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Iain H
authors.initials: IH
authors.lastname: Moal
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands.
authors.forename: Anna
authors.initials: A
authors.lastname: Vangone
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Brian G
authors.initials: BG
authors.lastname: Pierce
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands.
authors.forename: Panagiotis L
authors.initials: PL
authors.lastname: Kastritis
authors.affiliation: Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom.
authors.forename: Mieczyslaw
authors.initials: M
authors.lastname: Torchala
authors.affiliation: Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom.
authors.forename: Raphael
authors.initials: R
authors.lastname: Chaleil
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain.
authors.forename: Brian
authors.initials: B
authors.lastname: Jiménez-García
authors.affiliation: Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, London WC2A 3LY, United Kingdom. Electronic address: paul.bates@crick.ac.uk.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Bates
authors.affiliation: Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain. Electronic address: juan.fernandez@bsc.es.
authors.forename: Juan
authors.initials: J
authors.lastname: Fernandez-Recio
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584CH Utrecht, The Netherlands. Electronic address: a.m.j.j.bonvin@uu.nl.
authors.forename: Alexandre M J J
authors.initials: AM
authors.lastname: Bonvin
authors.affiliation: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: zhiping.weng@umassmed.edu.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D000818:Animals; D006801:Humans; D062105:Molecular Docking Simulation; D011062:Polynucleotide Adenylyltransferase / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D013816:Thermodynamics; D014616:Vaccinia virus / Q000737:chemistry / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D011506:Proteins; C088682:VP39 protein, Vaccinia virus; D014764:Viral Proteins; D011062:Polynucleotide Adenylyltransferase
keywords: antibody–antigen; binding free energy; conformational change; protein–protein complex structure; protein–protein interface