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Foldseek: fast and accurate protein structure search

View ORCID ProfileMichel van Kempen, View ORCID ProfileStephanie S. Kim, View ORCID ProfileCharlotte Tumescheit, View ORCID ProfileMilot Mirdita, View ORCID ProfileCameron L.M. Gilchrist, View ORCID ProfileJohannes Söding, View ORCID ProfileMartin Steinegger
doi: https://doi.org/10.1101/2022.02.07.479398
Michel van Kempen
1Quant. & Comput. Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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Stephanie S. Kim
2School of Biological Sciences, Seoul National University, Seoul, South Korea
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Charlotte Tumescheit
2School of Biological Sciences, Seoul National University, Seoul, South Korea
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  • ORCID record for Charlotte Tumescheit
Milot Mirdita
1Quant. & Comput. Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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  • ORCID record for Milot Mirdita
Cameron L.M. Gilchrist
2School of Biological Sciences, Seoul National University, Seoul, South Korea
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  • ORCID record for Cameron L.M. Gilchrist
Johannes Söding
1Quant. & Comput. Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
3Campus-Institute Data Science (CIDAS), Goldschmidtstrasse 1, 37077 Göttingen, Germany
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  • For correspondence: soeding@mpinat.mpg.de martin.steinegger@snu.ac.kr
Martin Steinegger
2School of Biological Sciences, Seoul National University, Seoul, South Korea
4Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
5Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
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  • For correspondence: soeding@mpinat.mpg.de martin.steinegger@snu.ac.kr
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Abstract

Highly accurate structure prediction methods are generating an avalanche of publicly available protein structures. Searching through these structures is becoming the main bottleneck in their analysis. Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being four to five orders of magnitude faster. Foldseek is free open-source software available at foldseek.com and as a webserver at search.foldseek.com.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Include ROC plot, HOMSTAD benchmark, and improved readability for color-blind readers

  • https://foldseek.com

  • https://search.foldseek.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 20, 2022.
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Foldseek: fast and accurate protein structure search
Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Cameron L.M. Gilchrist, Johannes Söding, Martin Steinegger
bioRxiv 2022.02.07.479398; doi: https://doi.org/10.1101/2022.02.07.479398
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Foldseek: fast and accurate protein structure search
Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Cameron L.M. Gilchrist, Johannes Söding, Martin Steinegger
bioRxiv 2022.02.07.479398; doi: https://doi.org/10.1101/2022.02.07.479398

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