Fast and accurate protein structure search with Foldseek

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...

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Bibliographic Details
Published in:Nature biotechnology Vol. 42; no. 2; pp. 243 - 246
Main Authors: van Kempen, Michel, Kim, Stephanie S., Tumescheit, Charlotte, Mirdita, Milot, Lee, Jeongjae, Gilchrist, Cameron L. M., Söding, Johannes, Steinegger, Martin
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01.02.2024
Nature Publishing Group
Subjects:
631/114
631/114/794
631/535
Agriculture
Amino acids
Bioinformatics
Biology
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Brief Communication
Life Sciences
Protein structure
Proteins
ISSN:1087-0156, 1546-1696, 1546-1696
Online Access:Get full text
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Summary: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.
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ISSN:1087-0156
1546-1696
1546-1696
DOI:10.1038/s41587-023-01773-0