ColabFold
Making Protein folding accessible to all via Google Colab!
- AlphaFold2_mmseqs2 -
monomers=Yes, homoligomers=Yes, mmseqs2=Yes, jackhmmer=No, templates=Yes
- AlphaFold2_complexes -
monomers=No, heterodimers=Yes, mmseqs2=Yes, jackhmmer=No, templates=No
- AlphaFold2_advanced -
monomers=Yes, homoligomers=Yes, mmseqs2=Yes, jackhmmer=Yes, templates=No
- RoseTTAFold -
monomers=Yes, homoligomers=No, mmseqs2=Yes, jackhmmer=No, templates=No
Official Notebook from Deepmind:
- AlphaFold2 -
monomers=Yes, homoligomers=No, mmseqs2=No, jackhmmer=Yes, templates=No
OLD Experimental notebooks:
- AlphaFold2_jackhmmer -
monomers=Yes, homoligomers=Yes, mmseqs2=Yes, jackhmmer=Yes, templates=No
- AlphaFold2_noTemplates_noMD
- AlphaFold2_noTemplates_yesMD
Maximum length limits depends on free GPU provided by Google-Colab fingers-crossed
- For GPU:
Tesla T4
orTesla 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
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?