Repositories list

• deepfold3-dev

  Public
  DeepFold 3: Biomolecular Complex Structure Prediction

  Python

  •

  MIT License

  •00 forks in DeepFoldProtein/deepfold3-dev•00 stars in DeepFoldProtein/deepfold3-dev•00 issues in DeepFoldProtein/deepfold3-dev•00 pull requests in DeepFoldProtein/deepfold3-dev•Updated Oct 29, 2026Oct 29, 2026

• DeepFold-PLM

  Public
  DeepFold-PLM

  Python

  •

  MIT License

  •00 forks in DeepFoldProtein/DeepFold-PLM•1212 stars in DeepFoldProtein/DeepFold-PLM•00 issues in DeepFoldProtein/DeepFold-PLM•00 pull requests in DeepFoldProtein/DeepFold-PLM•Updated Oct 3, 2026Oct 3, 2026

• OTalign

  Public
  OTalign: Protein sequence alignment for remote homologs using Protein Language Models and Unbalanced Optimal Transport.

  bioinformaticsdeep-learningcomputational-biology+ 4

  bioinformaticsdeep-learningcomputational-biologyoptimal-transportprotein-alignmentremote-homology-detectionprotein-language-models

  Python

  •00 forks in DeepFoldProtein/OTalign•55 stars in DeepFoldProtein/OTalign•00 issues in DeepFoldProtein/OTalign•00 pull requests in DeepFoldProtein/OTalign•Updated Sep 11, 2026Sep 11, 2026

• patchr

  Public
  Structure inpainting and simulation-ready setup for proteins, DNA, RNA, and complexes

  Python

  •

  MIT License

  •1010 forks in DeepFoldProtein/patchr•8181 stars in DeepFoldProtein/patchr•11 issue in DeepFoldProtein/patchr•00 pull requests in DeepFoldProtein/patchr•Updated Sep 5, 2026Sep 5, 2026

• plmMSA

  Public
  PLM-based MSA server. Rebase of DeepFoldProtein/PLMAlign.

  Python

  •

  MIT License

  •00 forks in DeepFoldProtein/plmMSA•00 stars in DeepFoldProtein/plmMSA•00 issues in DeepFoldProtein/plmMSA•00 pull requests in DeepFoldProtein/plmMSA•Updated Jul 24, 2026Jul 24, 2026

• MSA_FLOW

  Public
  Python

  •00 forks in DeepFoldProtein/MSA_FLOW•00 stars in DeepFoldProtein/MSA_FLOW•00 issues in DeepFoldProtein/MSA_FLOW•00 pull requests in DeepFoldProtein/MSA_FLOW•Updated May 10, 2026May 10, 2026

• ProteinTTT

  Public
  One protein is all you need (ICLR 2026)

  Jupyter Notebook

  •

  MIT License

  •1717 forks in DeepFoldProtein/ProteinTTT•00 stars in DeepFoldProtein/ProteinTTT•00 issues in DeepFoldProtein/ProteinTTT•00 pull requests in DeepFoldProtein/ProteinTTT•Updated Apr 6, 2026Apr 6, 2026

• pLM-BLAST

  Public
  Detection of remote homology by comparison of protein language model representations

  Python

  •

  MIT License

  •88 forks in DeepFoldProtein/pLM-BLAST•00 stars in DeepFoldProtein/pLM-BLAST•00 issues in DeepFoldProtein/pLM-BLAST•00 pull requests in DeepFoldProtein/pLM-BLAST•Updated Feb 27, 2026Feb 27, 2026

• EBA

  Public
  Python

  •

  Apache License 2.0

  •00 forks in DeepFoldProtein/EBA•00 stars in DeepFoldProtein/EBA•00 issues in DeepFoldProtein/EBA•00 pull requests in DeepFoldProtein/EBA•Updated Feb 27, 2026Feb 27, 2026

• dedal-fork

  Public
  Python

  •00 forks in DeepFoldProtein/dedal-fork•00 stars in DeepFoldProtein/dedal-fork•00 issues in DeepFoldProtein/dedal-fork•00 pull requests in DeepFoldProtein/dedal-fork•Updated Feb 27, 2026Feb 27, 2026

• proposals

  Public
  Python

  •00 forks in DeepFoldProtein/proposals•00 stars in DeepFoldProtein/proposals•00 issues in DeepFoldProtein/proposals•00 pull requests in DeepFoldProtein/proposals•Updated Feb 6, 2026Feb 6, 2026

• Protenix-MPS

  Public
  A trainable PyTorch reproduction of AlphaFold 3. (MPS version)

  Python

  •

  Apache License 2.0

  •331331 forks in DeepFoldProtein/Protenix-MPS•00 stars in DeepFoldProtein/Protenix-MPS•00 issues in DeepFoldProtein/Protenix-MPS•00 pull requests in DeepFoldProtein/Protenix-MPS•Updated Jan 10, 2026Jan 10, 2026

• recent-pdb

  Public
  Recent Protein Data Bank Entries

  Python

  •00 forks in DeepFoldProtein/recent-pdb•00 stars in DeepFoldProtein/recent-pdb•00 issues in DeepFoldProtein/recent-pdb•00 pull requests in DeepFoldProtein/recent-pdb•Updated Jan 7, 2026Jan 7, 2026

• cpm_kernels

  Public
  Python

  •

  Apache License 2.0

  •1010 forks in DeepFoldProtein/cpm_kernels•00 stars in DeepFoldProtein/cpm_kernels•00 issues in DeepFoldProtein/cpm_kernels•00 pull requests in DeepFoldProtein/cpm_kernels•Updated Sep 19, 2025Sep 19, 2025

• Pymol-Plugins

  Public
  Python

  •

  MIT License

  •00 forks in DeepFoldProtein/Pymol-Plugins•00 stars in DeepFoldProtein/Pymol-Plugins•00 issues in DeepFoldProtein/Pymol-Plugins•00 pull requests in DeepFoldProtein/Pymol-Plugins•Updated Aug 6, 2025Aug 6, 2025

• python-template

  Public template
  Python template repository

  Makefile

  •00 forks in DeepFoldProtein/python-template•00 stars in DeepFoldProtein/python-template•00 issues in DeepFoldProtein/python-template•00 pull requests in DeepFoldProtein/python-template•Updated Jul 14, 2025Jul 14, 2025

• af3-input

  Public
  AlphaFold 3 Input Generation with MMseqs2 and plmMSA

  Python

  •11 fork in DeepFoldProtein/af3-input•33 stars in DeepFoldProtein/af3-input•00 issues in DeepFoldProtein/af3-input•00 pull requests in DeepFoldProtein/af3-input•Updated Jun 12, 2025Jun 12, 2025

• DeepFold

  Public
  Framework for project DeepFold.

  protein-protein-interactionprotein-foldingprotein-structure-prediction

  protein-protein-interactionprotein-foldingprotein-structure-prediction

  Python

  •

  Apache License 2.0

  •00 forks in DeepFoldProtein/DeepFold•33 stars in DeepFoldProtein/DeepFold•00 issues in DeepFoldProtein/DeepFold•00 pull requests in DeepFoldProtein/DeepFold•Updated Jun 9, 2025Jun 9, 2025

• deepfold_v1

  Public
  Protein 3D Structure Prediction with DeepFold

  C

  •

  Apache License 2.0

  •33 forks in DeepFoldProtein/deepfold_v1•00 stars in DeepFoldProtein/deepfold_v1•00 issues in DeepFoldProtein/deepfold_v1•00 pull requests in DeepFoldProtein/deepfold_v1•Updated Jan 2, 2025Jan 2, 2025

• iitp-showcase

  Public
  Showcase

  Python

  •00 forks in DeepFoldProtein/iitp-showcase•00 stars in DeepFoldProtein/iitp-showcase•00 issues in DeepFoldProtein/iitp-showcase•00 pull requests in DeepFoldProtein/iitp-showcase•Updated Dec 12, 2024Dec 12, 2024

• trident

  Public
  A performance library for machine learning applications.

  Python

  •

  Apache License 2.0

  •1313 forks in DeepFoldProtein/trident•00 stars in DeepFoldProtein/trident•00 issues in DeepFoldProtein/trident•00 pull requests in DeepFoldProtein/trident•Updated Oct 12, 2023Oct 12, 2023

• .github

  Public
  Special repository for the organization's profile.

  00 forks in DeepFoldProtein/.github•00 stars in DeepFoldProtein/.github•00 issues in DeepFoldProtein/.github•00 pull requests in DeepFoldProtein/.github•Updated Aug 25, 2023Aug 25, 2023

• DeepFold_DB_docs

  Public
  HTML

  •00 forks in DeepFoldProtein/DeepFold_DB_docs•00 stars in DeepFoldProtein/DeepFold_DB_docs•00 issues in DeepFoldProtein/DeepFold_DB_docs•00 pull requests in DeepFoldProtein/DeepFold_DB_docs•Updated Aug 22, 2023Aug 22, 2023