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Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2
Open accessAbstract
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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Metadata
- 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
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2015-09
- Volume
- 427
- Issue
- 19
- Pages
- 3031-3041
- ISSN
- 0022-2836 (ISSN-L)
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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