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Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

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Vreven, Thom, Moal, Iain H., Vangone, Anna, Pierce, Brian G., Kastritis, Panagiotis L., Torchala, Mieczyslaw, Chaleil, Raphael, Jiménez-García, Brian, Bates, Paul A., Fernandez-Recio, Juan, Bonvin, Alexandre M.J.J., Weng, Zhiping·2015·Journal of Molecular Biology

DOI 10.1016/j.jmb.2015.07.016PMC PMC4677049

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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.

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Additional file 2 of Integrated structure-based protein interface prediction
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Additional file 1 of Classification of protein–protein association rates based on biophysical informatics
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Additional file 1 of Integrated structure-based protein interface prediction
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Authors: Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., Bonvin, A. M. J. J., & Weng, Z.
Affiliations: University of Massachusetts Chan Medical School (US)
Barcelona Supercomputing Center (ES)
Utrecht University (NL)
The Francis Crick Institute (GB)
Corresponding author: Bates, Paul A.
Bonvin, Alexandre M.J.J.
Weng, Zhiping
ORCID: Vreven, Thom
Moal, Iain H.
Vangone, Anna
Pierce, Brian G.
Kastritis, Panagiotis L.
Torchala, Mieczyslaw
Bates, Paul A.
Bonvin, Alexandre M.J.J.
Weng, Zhiping
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2015-09
Volume: 427
Issue: 19
Pages: 3031-3041
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2015.07.016
PMC: PMC4677049
OpenAlex: W1030883578
Cited by: 424
References: 70
Citations by year: 2026: 28 · 2025: 40 · 2024: 42 · 2023: 45 · 2022: 58 · 2021: 43 · 2020: 35 · 2019: 39 · 2018: 40 · 2017: 30 · 2016: 23
FWCI: 13.45
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (acceptedVersion, other-oa)
UPCommons institutional repository (Universitat Politècnica de Catalunya) (acceptedVersion, other-oa)
eScholarship@UMassChan (submittedVersion)
Utrecht University Repository (Utrecht University) (submittedVersion)
Figshare (submittedVersion, cc-by)
RECERCAT (Consorci de Serveis Universitaris de Catalunya) (submittedVersion, public-domain)
Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
Funders: Cancer Research UK (10748)
National Institute of General Medical Sciences (R01GM084884)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords: protein-protein docking, binding affinity prediction, docking benchmark, protein-protein complex, immune complexes, rigid-body docking
MeSH terms: Algorithms, Animals, Humans, Polynucleotide Adenylyltransferase, Protein Binding, Protein Conformation, Proteins, Software, Thermodynamics, Vaccinia virus, Viral Proteins, Protein Interaction Mapping, Molecular Docking Simulation

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Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

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