The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,723
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,111
Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80134-2 · Cited by 6,445
Jorgensen, W. L., & Tirado‐Rives, J. (1988) · Journal of the American Chemical Society · doi:10.1021/ja00214a001 · Cited by 5,060
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
Self-citationStatistical potential for assessment and prediction of protein structures
Shen, M., & Šali, A. (2006) · Protein Science · doi:10.1110/ps.062416606 · Cited by 2,294
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
Pierce, B. G., Wiehe, K. J., Hwang, H., Kim, B., Vreven, T., & Weng, Z. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu097 · Cited by 1,767
Self-citationZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393
Self-citation
Cited by
Sorted by citations
Improved prediction of protein-protein interactions using AlphaFold2
Bryant, P., Pozzati, G., & Elofsson, A. (2021) · doi:10.1101/2021.09.15.460468 · Cited by 1,022
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Gaínza, P., Sverrisson, F., Monti, F., Rodolà, E., Boscaini, D., Bronstein, M. M., & Correia, B. E. (2019) · Nature Methods · doi:10.1038/s41592-019-0666-6 · Cited by 839
Performance and Its Limits in Rigid Body Protein-Protein Docking
Desta, I., Porter, K. A., Xia, B., Kozakov, D., & Vajda, S. (2020) · Structure · doi:10.1016/j.str.2020.06.006 · Cited by 709
Key Topics in Molecular Docking for Drug Design
Torres, P. H. M., Sodero, A. C. R., Jofily, P., & Silva, F. P. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184574 · Cited by 703
Protein interface prediction using graph convolutional networks
Fout, A., Ben‐Hur, A., Anderson, C., Chitsaz, H., & Zhou, W. (2017) · Digital Collections of Colorado (Colorado State University) · doi:10.25675/3.021826 · Cited by 606
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 ›
Are you an author, or do you see a problem with this page? Request a review
