ColabFold

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- 16Aug2021: WARNING - MMseqs2 API is undergoing upgrade, you may see error messages.
+ 17Aug2021: Things are looking stable now! If you see any errors, please report them.
- 17Aug2021: We are still debugging the MSA generation procedure... there might be some differences between the old/new run.

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Making Protein folding accessible to all via Google Colab!

Notebooks	monomers	complexes	mmseqs2	jackhmmer	templates
AlphaFold2_mmseqs2	Yes	No	Yes	No	Yes
AlphaFold2_advanced	Yes	Yes	Yes	Yes	No
RoseTTAFold	Yes	No	Yes	No	No
AlphaFold2 (from Deepmind)	Yes	No	No	Yes	No
OLD retired notebooks	monomers	complexes	mmseqs2	jackhmmer	templates
AlphaFold2_complexes	No	Yes	No	No	No
AlphaFold2_jackhmmer	Yes	No	Yes	Yes	No
AlphaFold2_noTemplates_noMD
AlphaFold2_noTemplates_yesMD

FAQ

• Can I use the models for Molecular Replacement?
  • Yes, but be CAREFUL, the bfactor column is populated with pLDDT confidence values (higher = better). Phenix.phaser expects a "real" bfactor, where (lower = better). See post from Claudia Millán.
• What is the maximum length?
  • Limits depends on free GPU provided by Google-Colab fingers-crossed
  • For GPU: Tesla T4 or Tesla P100 with ~16G the max length is ~1400
  • For GPU: Tesla K80 with ~12G the max length is ~1000
  • To check what GPU you got, open a new code cell and type !nvidia-smi

Tutorials & Presentations

• ColabFold Tutorial presented at the Boston Protein Design and Modeling Club. [video] [slides].

Acknowledgments

• We would like to thank the RoseTTAFold and AlphaFold team for doing an excellent job open sourcing the software.
• Also credit to David Koes for his awesome py3Dmol plugin, without whom these notebooks would be quite boring!
• A colab by Sergey Ovchinnikov (@sokrypton), Milot Mirdita (@milot_mirdita) and Martin Steinegger (@thesteinegger).

How do I reference this work?

Mirdita M, Ovchinnikov S and Steinegger M. ColabFold - Making protein folding accessible to all.
bioRxiv, doi: 10.1101/2021.08.15.456425 (2021)