3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources
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Abstract
While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank.
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- Authors
- Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., Hatos, A., Hegedus, T., Hekkelman, M. L., Joosten, R., Jumper, J., Laydon, A., Molodenskiy, D., Piovesan, D., Salladini, E., Salzberg, S. L., Sommer, M. J., Steinegger, M., Suhajda, E., Svergun, D., Tenorio-Ku, L., Tosatto, S., Tunyasuvunakool, K., Waterhouse, A. M., Žídek, A., Schwede, T., Orengo, C., & Velankar, S.
- Affiliations
- European Molecular Biology Laboratory, European Bioinformatics Institute , Hinxton CB10 1SA,
- European Bioinformatics Institute (GB)
- University College London (GB)
- SIB Swiss Institute of Bioinformatics (CH)
- Google DeepMind (United Kingdom) (GB)
- Department of Biomedical Sciences , University of Padova, Padova 35129,
- Department of Biophysics and Radiation Biology , Semmelweis University, Budapest 1094,
- The Netherlands Cancer Institute (NL)
- University of Padua (IT)
- Johns Hopkins University (US)
- Seoul National University (KR)
- ORCID
- Varadi, Mihaly
- Nair, Sreenath
- Sillitoe, Ian
- Tauriello, Gerardo
- Anyango, Stephen
- Bienert, Stefan
- Borges, Clemente
- Deshpande, Mandar
- Green, Tim
- Hassabis, Demis
- Hatos, Andras
- Hegedus, Tamas
- Hekkelman, Maarten L
- Joosten, Robbie
- Jumper, John
- Laydon, Agata
- Molodenskiy, Dmitry
- Piovesan, Damiano
- Salladini, Edoardo
- Salzberg, Steven L
- Sommer, Markus J
- Steinegger, Martin
- Suhajda, Erzsebet
- Svergun, Dmitri
- Tenorio-Ku, Luiggi
- Tosatto, Silvio
- Tunyasuvunakool, Kathryn
- Waterhouse, Andrew Mark
- Žídek, Augustin
- Schwede, Torsten
- Orengo, Christine
- Velankar, Sameer
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2022
- Volume
- 11
- ISSN
- 2047-217X (ISSN-L)
- PMC
- PMC9709962
- OpenAlex
- W4311287562
- Cited by
- 32
- References
- 46
- Citations by year
- 2026: 6 · 2025: 11 · 2024: 5 · 2023: 9 · 2022: 1
- FWCI
- 2.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- GigaScience (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- SERVAL (Université de Lausanne) (publishedVersion, cc-by)
- edoc (University of Basel) (acceptedVersion)
- IRIS (submittedVersion, cc-by)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/S020071/1)
- National Research Foundation (2021-R1C1-C102065)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein structure prediction, federated data network, comparative model evaluation, Protein Data Bank
- MeSH terms
- Metadata, Amino Acid Sequence, Computer Simulation, Records, Databases, Protein
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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