๐ Table of contents
๐ก Notes
- The following lists are curated by humans, as such may be incomplete
- We only include software targeting the folding problem combining learnings from AlphaFold 2 and protein language models. You may find other ML on protein tools at Kevin's incredible ML for proteins list.
- We do not wish to advertize one tool over any other, but simply list the tools we are aware of in either random or alphabetical order
- Any suggestions for improvements and additions are welcome as issues or pull requests
- Projects we identify as discontinued are marked with ๐
โก๏ธ Brought to you by:
[in alphabetical order]
-
MSA-based (uses Multiple Sequence Alignment as input)
- AlphaFold2 (JAX)
- ColabFold (JAX - faster AF2 compiling and MSA generations)
- FastFold (Pytorch)
- Manuscript: https://arxiv.org/abs/2203.00854
- Code: https://github.com/hpcaitech/FastFold
- HelixFold (PaddlePaddle)
- MineSpore-Fold (mindspore)
- OpenFold (PyTorch)
- Manuscript?
- Code: https://github.com/aqlaboratory/openfold
- RoseTTAFold (PyTorch)
- Uni-Fold (PyTorch/JAX)
- Manuscript: https://doi.org/10.1101/2022.08.04.502811
- Code (PyTorch): https://github.com/dptech-corp/Uni-Fold
- Code (JAX): https://github.com/dptech-corp/Uni-Fold-jax
-
pLM-based (uses Protein Language Model as input)
- ESM-Fold (PyTorch)
- Manuscript: https://doi.org/10.1101/2022.07.20.500902
- Code: ? (potentially: https://github.com/facebookresearch/esm)
- Other: [tweet] Alex's announcement,
- EMBER3D (PyTorch):
- Manuscript: ?
- Code: https://github.com/kWeissenow/EMBER3D
- HelixFold-single (PaddlePaddle)
- OmegaFold (PyTorch)
- ESM-Fold (PyTorch)
- DeepAB (PyTorch)
- IgFold (PyTorch)
- gget (AF2)
- ๐ Lucidrains AF2 (AF2)
- ๐ Lupoglaz OpenFold2 (AF2)
- alphafold_finetune - finetune AlphaFold for Protein-Peptide prediction
- AlphaPulldown - protein-protein interaction screens using AlphaFold-Multimer
- ColabDesign - Backprop through AlphaFold for protein design
- AF2Rank - Rank Decoy Structures/Sequences using AlphaFold
- Manuscript: https://www.biorxiv.org/content/10.1101/2022.03.11.484043v3
- Code: https://github.com/jproney/AF2Rank
- Resource: Colab Notebook
- AlphaFold Database (UniRef90 | AF2)
- Manuscript: https://doi.org/10.1093/nar/gkab1061
- Resource: https://alphafold.ebi.ac.uk
- Eukaryotic interactormes (Protein-Protein interactions | RF/AF2)
- Structures of human-transcriptome isoforms (ColabFold/AF2)
- Manuscript: https://doi.org/10.1101/2022.06.08.495354
- Resource: https://www.isoform.io
- AlphaFill - enriching the AlphaFold models with ligands and co-factors (AF2)
- Manuscript: https://www.biorxiv.org/content/10.1101/2021.11.26.470110v1
- Resource: https://alphafill.eu/
- IgFold Database (OAS | IgFold)
- Lambda PredictProtein (ColabFold|limit:500AA)
- Manuscript: https://doi.org/10.1101/2022.08.04.502750
- Resource: http://embed.predictprotein.org/
- ๐ Moonbear
- Resource: https://www.getmoonbear.com/
- Other: [tweet] Stephanie's announcement