Abstract

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.

Keywords

BottleneckAlphabetComputer scienceComputationProtein structureProtein tertiary structureComputational biologyInformation retrievalAlgorithmChemistryBiologyBiochemistry

MeSH Terms

AlgorithmsDatabasesProteinProteinsAmino AcidsSoftware

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Publication Info

Year
2023
Type
article
Volume
42
Issue
2
Pages
243-246
Citations
1825
Access
Closed

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Cite This

Michel van Kempen, Stephanie Kim, Charlotte Tumescheit et al. (2023). Fast and accurate protein structure search with Foldseek. Nature Biotechnology , 42 (2) , 243-246. https://doi.org/10.1038/s41587-023-01773-0

Identifiers

DOI
10.1038/s41587-023-01773-0
PMID
37156916
PMCID
PMC10869269

Data Quality

Data completeness: 90%