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Journal Article

Fast and accurate protein structure search with Foldseek

MPS-Authors
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van Kempen,  Michel
Research Group of Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society;

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Mirdita,  Milot
Research Group of Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society;

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Söding,  Johannes       
Research Group of Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society;

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s41587-023-01773-0.pdf
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Citation

van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., et al. (2024). Fast and accurate protein structure search with Foldseek. Nature Biotechnology, 42, 243-246. doi:10.1038/s41587-023-01773-0.


Cite as: https://hdl.handle.net/21.11116/0000-000D-5460-8
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.