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📖 Table of contents

💡 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 💀 and in a section at the end

⚡️ Brought to you by:

Predictors

[in alphabetical order]

  • MSA-based (uses Multiple Sequence Alignments (MSAs) as input)

    • AlphaFold2
      • The original AlphaFold 2 method
      • Features: monomer, multimer
      • Other: Colab Notebook
    • ColabFold
      • Faster AF2 compiling and MSA generations
      • Features: monomer, multimer
      • Other: localcolabfold
    • FastFold
      • Runtime improvements to OpenFold (see below)
      • Features: monomer
    • HelixFold
      • Reimplementation of AF2 in PaddlePaddle
      • Features: monomer
    • MEGA-Fold
      • Reimplementation of AF2 in MindSpore; provides training code, training dataset and new model params.
      • Features: monomer
    • OpenFold
      • Reimplementation of AF2 in PyTorch; provides training code, training dataset and new model params.
      • Features: monomer
      • Other: Colab Notebook
    • RoseTTAFold
      • Reproduced AF2 in PyTorch before details of AF2 were available; new model parameters.
      • Features: monomer
      • Other: Unofficial Colab Notebook
    • Uni-Fold
      • Reimplementation of AF2 in PyTorch; provides training code and new (monomer/multimer) model parameters.
      • Features: monomer, multimer
      • Resources: Colab Notebook
    • Uni-Fold-jax
      • Implementation of AF2's training code.

  • pLM-based (using embeddings from protein Language Models (pLMs) as input)

  • Other

    • EquiFold
      • Diffusion model to predict protein structures (specifically antibodies)
      • Features: monomer

  • Conformational change and dynamics (TODO)

    • AFcluster
    • AFsample
    • etc

  • AlphaFold3 and friends

Tools and Extensions

  • gget (AF2)
  • alphafold_finetune
  • AlphaPulldown
    • protein-protein interaction screens using AlphaFold-Multimer
  • ColabDesign
    • Backprop through AlphaFold for protein design
  • AF2Rank
    • Rank Decoy Structures/Sequences using AlphaFold
    • Resource: Colab Notebook
  • protein_structure_module_of_AF2
    • IPA implementation in pytorch

Databases of predictions

Datasets for training

Webservers

Discontinued