The DOI matches its Crossref record.
Protein–protein docking benchmark version 3.0
Open accessAbstract
We present version 3.0 of our publicly available protein–protein docking benchmark. This update includes 40 new test cases, representing a 48% increase from Benchmark 2.0. For all of the new cases, the crystal structures of both binding partners are available. As with Benchmark 2.0, Structural Classification of Proteins (Murzin et al., J Mol Biol 1995;247:536–540) was used to remove redundant test cases. The 124 unbound‐unbound test cases in Benchmark 3.0 are classified into 88 rigid‐body cases, 19 medium‐difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. In addition to providing the community with more test cases for evaluating docking methods, the expansion of Benchmark 3.0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark. Proteins 2008. © 2008 Wiley‐Liss, Inc.
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
Cited by
The ClusPro web server for protein–protein docking
Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017) · Nature Protocols · doi:10.1038/nprot.2016.169 · Cited by 3,310
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., et al. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.07.016 · Cited by 424
Self-citationProtein–protein interaction and quaternary structure
Janin, J., Bahadur, R. P., & Chakrabarti, P. (2008) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583508004708 · Cited by 398
Self-citationCPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK
de Vries, S. J., & Bonvin, A. M. J. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017695 · Cited by 324
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., & Gray, J. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022477 · Cited by 310
Metadata
- Authors
- Hwang, H., Pierce, B., Mintseris, J., Janin, J., & Weng, Z.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2008-05-19
- Volume
- 73
- Issue
- 3
- Pages
- 705-709
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2162682281
- Cited by
- 255
- References
- 0
- FWCI
- 10.79
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Protein–protein docking benchmark version 3.0. https://app.cochat.ai/papers/10.1002/prot.22106
- The paper
- Hwang, H., Pierce, B., Mintseris, J., Janin, J., & Weng, Z. (2008). Protein–protein docking benchmark version 3.0. Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.22106
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
