---
title: "Provenance-backed protein model enrichment batch."
task: ""
lineage_type: import
upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/enrichment.protein-v2.yml
upstream_sha: 7a064bf0
imported_at: 2026-08-08
prompt_class: catalogue
upstream_changes: accepted
author: upstream
validated: false
---

# Provenance-backed protein model enrichment batch.
resources:
  esm3:
    entities: [protein]
    methods: [generative-model, language-model, transformer]
    modalities: [molecular-structure, protein-sequence]
    tasks: [protein-sequence-design, representation-learning]
    github: https://github.com/evolutionaryscale/esm
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/evolutionaryscale/esm

  evolutionary_scale_modeling_esm:
    entities: [protein]
    methods: [language-model, self-supervised-learning, transformer]
    modalities: [protein-sequence]
    tasks: [representation-learning]
    github: https://github.com/facebookresearch/esm
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/facebookresearch/esm

  prottrans:
    entities: [protein]
    methods: [language-model, self-supervised-learning, transformer]
    modalities: [protein-sequence]
    tasks: [representation-learning]
    github: https://github.com/agemagician/ProtTrans
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/agemagician/ProtTrans

  progen2:
    entities: [protein]
    methods: [generative-model, language-model, transformer]
    modalities: [protein-sequence]
    tasks: [protein-sequence-design, representation-learning]
    github: https://github.com/salesforce/progen
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/salesforce/progen

  alphafold3:
    entities: [molecule, protein, protein-complex]
    methods: [diffusion]
    modalities: [molecular-structure, protein-sequence]
    tasks: [structure-prediction]
    github: https://github.com/google-deepmind/alphafold3
    last_checked: 2026-08-08
    metadata_sources:
      - https://github.com/google-deepmind/alphafold3