The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Structural motif search across the protein-universe with Folddisco
Open accessPreprint — published as 10.1038/s41587-026-03162-9 · Paper page
Abstract
Detecting similar protein structural motifs, functionally crucial short 3D patterns, in large structure collections is computationally prohibitive. Therefore, we developed Folddisco, which overcomes this through an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco’s compact 1.45-terabyte index of 53 million AFDB50 structures enables querying this database within seconds. It is up to 20-fold faster in querying and 4-fold more storage-efficient than existing methods. Folddisco is more accurate and storage-efficient than state-of-the-art methods, while being an order of magnitude faster. Folddisco is free software available at https://folddisco.foldseek.com and a webserver at https://search.foldseek.com/folddisco.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Self-citationVaradi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052
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Metadata
- Authors
- Steinegger, M., Kim, H., Kim, R. S., & Mirdita, M.
- Affiliations
- Seoul National University (KR)
- Corresponding author
- Steinegger, Martin
- Venue
- Nature Biotechnology
- Published
- 2025-08-07
- ISSN
- 0733-222X (ISSN-L)
- OpenAlex
- W4412065994
- Cited by
- 10
- References
- 2
- Citations by year
- 2026: 9 · 2025: 1
- FWCI
- 18.47
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Biotechnology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Research Foundation
- Seoul National University
- National Research Foundation of Korea (RS-2020-NR049543, RS-2021-NR061659, 2020M3‐A9G7‐103933, RS-2024-00396026, RS-2023-00250470, RS-2021-NR056571, RS-2025-25405694)
- Novo Nordisk
- Novo Nordisk Fonden (NNF24SA0092560)
- Samsung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- side chain orientation, protein structure database, protein structure comparison, web server
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