https://github.com/animesh/folding_tools
A collection of *fold* tools
Science Score: 23.0%
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✓DOI references
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Low similarity (11.0%) to scientific vocabulary
Last synced: 10 months ago
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Repository
A collection of *fold* tools
Basic Info
- Host: GitHub
- Owner: animesh
- License: mit
- Default Branch: main
- Size: 141 KB
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- Forks: 0
- Open Issues: 0
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Fork of biolists/folding_tools
Created over 3 years ago
· Last pushed over 3 years ago
https://github.com/animesh/folding_tools/blob/main/
**Table of contents** * [Predictors](#Predictors) * [Tools and Extensions](#Tools) * [Databases and Datasets](#Databases) * [Webservers](#Webservers) * [Discontinued](#Discontinued) **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](https://github.com/yangkky/Machine-learning-for-proteins). - 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 and in a section at the end **Brought to you by:** - [@sacdallago](https://twitter.com/sacdallago) - [@sokrypton](https://twitter.com/sokrypton) ---- ### Predictors [_in alphabetical order_] - **MSA-based** (uses Multiple Sequence Alignments (MSAs) as input) - AlphaFold2 [](https://github.com/deepmind/alphafold) [](https://www.nature.com/articles/s41586-021-03819-2) - The original AlphaFold 2 method - Features: monomer, multimer - Other: [Colab Notebook](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb) - ColabFold [](https://github.com/sokrypton/ColabFold) [](https://www.nature.com/articles/s41592-022-01488-1) - Faster AF2 compiling and MSA generations - Features: monomer, multimer - Other: [localcolabfold](https://github.com/YoshitakaMo/localcolabfold) - FastFold [](https://github.com/hpcaitech/FastFold) [](https://arxiv.org/abs/2203.00854) - Runtime improvements to OpenFold (see below) - Features: monomer - HelixFold [](https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold) [](https://arxiv.org/abs/2207.05477) - Reimplementation of AF2 in PaddlePaddle - Features: monomer - MEGA-Fold [](https://gitee.com/mindspore/mindscience/tree/master/MindSPONGE/applications/MEGAProtein) [](https://arxiv.org/abs/2206.12240) - Reimplementation of AF2 in MindSpore; provides training code, training dataset and new model params. - Features: monomer - OpenFold [](https://github.com/aqlaboratory/openfold) - Reimplementation of AF2 in PyTorch; provides training code, training dataset and new model params. - Features: monomer - Other: [Colab Notebook](https://colab.research.google.com/github/aqlaboratory/openfold/blob/main/notebooks/OpenFold.ipynb) - RoseTTAFold [](https://github.com/RosettaCommons/RoseTTAFold) [](https://www.science.org/doi/10.1126/science.abj8754) - Reproduced AF2 in PyTorch before details of AF2 were available; new model parameters. - Features: monomer - Other: [Unofficial Colab Notebook](https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/RoseTTAFold.ipynb) - Uni-Fold [](https://github.com/dptech-corp/Uni-Fold) [](https://doi.org/10.1101/2022.08.04.502811) - Reimplementation of AF2 in PyTorch; provides training code and new (monomer/multimer) model parameters. - Features: monomer, multimer - Resources: [Colab Notebook](https://colab.research.google.com/github/dptech-corp/Uni-Fold/blob/main/notebooks/unifold.ipynb) - Uni-Fold-jax [](https://github.com/dptech-corp/Uni-Fold-jax) [](https://doi.org/10.1101/2022.08.04.502811) - Implementation of AF2's training code. - **pLM-based** (using embeddings from protein Language Models (pLMs) as input) - ESM-Fold [](https://doi.org/10.1101/2022.07.20.500902) - Features: monomer - Other: [[tweet] Alex's announcement](https://twitter.com/alexrives/status/1550148755206414341) - EMBER3D [](ttps://github.com/kWeissenow/EMBER3D) - Features: monomer - HelixFold-single [](https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold-single) [](https://arxiv.org/abs/2207.13921) - Features: monomer - Resource: https://paddlehelix.baidu.com/app/drug/protein-single/forecast - IgFold [](https://github.com/Graylab/IgFold) [](https://doi.org/10.1101/2022.04.20.488972) - pLM focused on antibody sequences - Features: monomer - Other: [Colab Notebook](https://colab.research.google.com/github/Graylab/IgFold/blob/main/IgFold.ipynb) - OmegaFold [](https://github.com/HeliXonProtein/OmegaFold) [](https://doi.org/10.1101/2022.07.21.500999) - Features: monomer - Other: [Unofficial Colab Notebook](https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/omegafold.ipynb), [[tweet] Martin comparing structures](https://twitter.com/thesteinegger/status/1554881669718573062), [[tweet] Sergey's positional encoding observation](https://twitter.com/sokrypton/status/1555536325176168448) - **Other** - EquiFold [](https://doi.org/10.1101/2022.10.07.511322) - Diffusion model to predict protein structures (specifically antibodies) - Features: monomer ### Tools and Extensions - gget (AF2) [](https://github.com/pachterlab/gget#gget-alphafold- ) [](https://doi.org/10.1101/2022.05.17.492392) - alphafold_finetune [](https://github.com/phbradley/alphafold_finetune) [](https://doi.org/10.1101/2022.07.12.499365) - finetune AlphaFold for Protein-Peptide prediction - Other: [[tweet] Amir's announcement](https://twitter.com/AMotmaen/status/1547435940011945984) - AlphaPulldown [](https://www.embl-hamburg.de/AlphaPulldown/) [](https://doi.org/10.1101/2022.08.05.502961) - protein-protein interaction screens using AlphaFold-Multimer - ColabDesign [](https://github.com/sokrypton/ColabDesign) - Backprop through AlphaFold for protein design - AF2Rank [](https://github.com/jproney/AF2Rank) [](https://doi.org/10.1101/2022.03.11.484043) - Rank Decoy Structures/Sequences using AlphaFold - Resource: [Colab Notebook](https://colab.research.google.com/github/sokrypton/ColabDesign/blob/main/af/examples/AF2Rank.ipynb) - protein_structure_module_of_AF2 [](https://github.com/pengzhangzhi/protein_structure_module_of_AF2) - IPA implementation in pytorch ---- ### Databases of predictions - AlphaFold Database [](https://doi.org/10.1093/nar/gkab1061) - All sequences in UniRef90 - viral sequences; Based on AlphaFold 2 - Resource: https://alphafold.ebi.ac.uk - Eukaryotic interactormes [](https://www.science.org/doi/10.1126/science.abm4805) - Protein-Protein interactions; Based on RoseTTAFold and AlphaFold 2 - Resource: https://www.ebi.ac.uk/pdbe/news/predicted-complexes-modelarchive-now-pdbe-kb-pages - Structures of human-transcriptome isoforms [](https://doi.org/10.1101/2022.06.08.495354) - Based on ColabFold (AlphaFold 2) - Resource: https://www.isoform.io - AlphaFill [](https://doi.org/10.1101/2021.11.26.470110) - Enriching the AlphaFold models with ligands and co-factors (AlphaFold 2) - Resource: https://alphafill.eu/ - IgFold Database [](https://doi.org/10.1101/2022.04.20.488972) - Predictions specific to antibody sequences; based on OAS dataset and IgFold - Resource: https://data.graylab.jhu.edu/igfold_oas_paired95.tar.gz ### Datasets for training - OpenFold - MSAs for 132K PDBs + 270K UniClust30 predictions for distilation - Resource: https://registry.opendata.aws/openfold/ - MindSpore - MSAs for 570K PDBs + 745K Distillation - Manuscript: https://arxiv.org/abs/2206.12240 - Resource: http://ftp.cbi.pku.edu.cn/psp/ ---- ### Webservers - Lambda PredictProtein [](https://doi.org/10.1101/2022.08.04.502750) - Based on ColabFold; Limited to sequences up to 500AAs - Resource: http://embed.predictprotein.org/ - Robetta - Based on RoseTTAFold - Resource: https://robetta.bakerlab.org/ ---- ### Discontinued - Moonbear - Resource: https://www.getmoonbear.com/ - Other: [[tweet] Stephanie's announcement](https://twitter.com/stephanieszhang/status/1427773598199164937) - Lucidrains' AlphaFold2 [](https://github.com/lucidrains/alphafold2) - AF2 reproduction attempt - Features: monomer - Lupoglaz's OpenFold2 [](https://github.com/lupoglaz/OpenFold2) - AF2 reproduction attempt - Features: monomer
Owner
- Name: Ani
- Login: animesh
- Kind: user
- Location: Norway
- Company: Norwegian University of Science and Technology
- Website: https://www.fuzzylife.org
- Twitter: animesh1977
- Repositories: 749
- Profile: https://github.com/animesh
A medical graduate from Delhi University with post-graduation in bioinformatics from Jawaharlal Nehru University, India.