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Fast and accurate protein structure search with Foldseek
Open accessPreprint — published as 10.1038/s41587-023-01773-0 · Paper page
Abstract
As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing the amino acid backbone of proteins as sequences over a structural alphabet. Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of DALI, TM-align and CE, respectively.
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Metadata
- Authors
- van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M.
- Affiliations
- Max Planck Institute for Multidisciplinary Sciences (DE)
- Seoul National University (KR)
- Corresponding author
- Söding, Johannes
- Steinegger, Martin
- ORCID
- Venue
- Nature Biotechnology
- Publisher
- openRxiv
- Published
- 2022-02-09
- Volume
- 42
- Issue
- 2
- Pages
- 243-246
- ISSN
- 0733-222X (ISSN-L)
- PMC
- PMC10869269
- OpenAlex
- W4375858802
- Cited by
- 2,598
- References
- 48
- Citations by year
- 2026: 830 · 2025: 917 · 2024: 592 · 2023: 211 · 2022: 44
- FWCI
- 226.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Nature Biotechnology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- National Research Foundation
- Bundesministerium für Bildung und Forschung
- Seoul National University
- National Research Foundation of Korea (2021-R1C1-C102065, 2019R1A6A1A10073437, 2020M3A9G7103933, 2021R1C1C102065, 2021M3A9I4021220, 2021-M3A9-I4021220, 2020M3‐A9G7‐103933, 2019R1A6A1, 2019R1-A6A1-A10073437)
- Max-Planck-Gesellschaft
- 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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- protein structure search, Foldseek, structural alignment, structural alphabet, protein structure database, computational efficiency
- MeSH terms
- Algorithms, Amino Acids, Proteins, Software, Databases, Protein
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