Fast and accurate protein structure search with Foldseek.

Autor: van Kempen M; Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Kim SS; School of Biological Sciences, Seoul National University, Seoul, South Korea., Tumescheit C; School of Biological Sciences, Seoul National University, Seoul, South Korea., Mirdita M; Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.; School of Biological Sciences, Seoul National University, Seoul, South Korea., Lee J; School of Biological Sciences, Seoul National University, Seoul, South Korea., Gilchrist CLM; School of Biological Sciences, Seoul National University, Seoul, South Korea., Söding J; Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. soeding@mpinat.mpg.de.; Campus Institute Data Science (CIDAS), Göttingen, Germany. soeding@mpinat.mpg.de., Steinegger M; School of Biological Sciences, Seoul National University, Seoul, South Korea. martin.steinegger@snu.ac.kr.; Artificial Intelligence Institute, Seoul National University, Seoul, South Korea. martin.steinegger@snu.ac.kr.; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea. martin.steinegger@snu.ac.kr.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2024 Feb; Vol. 42 (2), pp. 243-246. Date of Electronic Publication: 2023 May 08.
DOI: 10.1038/s41587-023-01773-0
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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