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ColabFold - Making protein folding accessible to all

View ORCID ProfileMilot Mirdita, View ORCID ProfileSergey Ovchinnikov, View ORCID ProfileMartin Steinegger
doi: https://doi.org/10.1101/2021.08.15.456425
Milot Mirdita
1Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Sergey Ovchinnikov
2JHDSF Program, Harvard University, Cambridge, MA 02138, USA
3FAS Division of Science, Harvard University, Cambridge, MA 02138, USA
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Martin Steinegger
4School of Biological Sciences, Seoul National University, Seoul, South Korea
5Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
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  • For correspondence: martin.steinegger@snu.ac.kr
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Summary

ColabFold is an easy-to-use Notebook based environment for fast and convenient protein structure predictions. Its structure prediction is powered by AlphaFold2 and RoseTTAFold combined with a fast multiple sequence alignment generation stage using MMseqs2. MMseqs2’s MSAs produce more accurate predictions while being ~16 faster compared to the AlphaFold2’s MSA stage. ColabFold also offers many advanced features, such as homo- and hetero-complex modeling and exposes AlphaFold2 internals. When coupled with Google Colab, ColabFold becomes a free and accessible platform for protein folding that does not require any installation or expensive hardware.

Code ColabFold is free open-source (MIT) [1] software available at https://github.com/sokrypton/ColabFold.

Contact milot.mirdita{at}mpibpc.mpg.de, so{at}fas.harvard.edu, martin.steinegger{at}snu.ac.kr

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/sokrypton/ColabFold

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-NC-ND 4.0 International license.
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Posted August 15, 2021.
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ColabFold - Making protein folding accessible to all
Milot Mirdita, Sergey Ovchinnikov, Martin Steinegger
bioRxiv 2021.08.15.456425; doi: https://doi.org/10.1101/2021.08.15.456425
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ColabFold - Making protein folding accessible to all
Milot Mirdita, Sergey Ovchinnikov, Martin Steinegger
bioRxiv 2021.08.15.456425; doi: https://doi.org/10.1101/2021.08.15.456425

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