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  Fast and accurate protein structure search with Foldseek

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.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000D-5460-8 Version Permalink: https://hdl.handle.net/21.11116/0000-000F-2258-8
Genre: Journal Article

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s41587-023-01773-0.pdf (Publisher version), 7MB
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 Creators:
van Kempen, Michel1, Author           
Kim, Stephanie S., Author
Tumescheit, Charlotte, Author
Mirdita, Milot1, Author           
Lee, Jeongjae, Author
Gilchrist, Cameron L. M., Author
Söding, Johannes1, Author                 
Steinegger, Martin, Author
Affiliations:
1Research Group of Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society, ou_3350226              

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 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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Language(s): eng - English
 Dates: 2023-05-082024-02
 Publication Status: Issued
 Pages: -
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 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41587-023-01773-0
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Project name : M.S. acknowledges support from the National Research Foundation of Korea (NRF) (grants 2019R1A6A1A10073437, 2020M3A9G7103933, 2021R1C1C102065 and 2021M3A9I4021220), the Samsung DS Research Fund and the Creative-Pioneering Researchers Program through Seoul National University. S.K. acknowledges support by NRF grant 2019R1A6A1A10073437. J.S. acknowledges support by the German Ministry for Education and Research (horizontal4meta).
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Title: Nature Biotechnology
  Abbreviation : Nat. Biotechnol.
Source Genre: Journal
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Publ. Info: New York : Gale Group Inc.
Pages: - Volume / Issue: 42 Sequence Number: - Start / End Page: 243 - 246 Identifier: ISSN: 1087-0156
CoNE: https://pure.mpg.de/cone/journals/resource/954926980065