# Fast and accurate protein structure search with Foldseek

“Fast and accurate protein structure search with Foldseek” (2023), by Michel van Kempen et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

- Authors: Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeong-Jae Lee, Cameron L. M. Gilchrist, Johannes Söding, Martin Steinegger
- Published: May 8, 2023
- Field: Genetics and Biochemistry
- DOI: https://doi.org/10.1038/s41587-023-01773-0
- Free PDF: https://www.nature.com/articles/s41587-023-01773-0.pdf

## 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.

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