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Fast and accurate protein structure search with Foldseek

Cited 150 time in Web of Science Cited 140 time in Scopus
Authors

van Kempen, Michel; Kim, Stephanie S.; Tumescheit, Charlotte; Mirdita, Milot; Lee, Jeongjae; Gilchrist, Cameron L. M.; Soeding, Johannes; Steinegger, Martin

Issue Date
2024-02
Publisher
Nature Publishing Group
Citation
Nature Biotechnology, Vol.42 No.2, pp.243-246
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 tertiary amino acid interactions within 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. Foldseek speeds up protein structural search by four to five orders of magnitude.
ISSN
1087-0156
URI
https://hdl.handle.net/10371/202486
DOI
https://doi.org/10.1038/s41587-023-01773-0
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  • College of Natural Sciences
  • School of Biological Sciences
Research Area Development of algorithms to search, cluster and assemble sequence data, Metagenomic analysis, Pathogen detection in sequencing data

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