{
  "schema_version": 1,
  "updated": "2026-08-30",
  "verification_policy": "Pins were checked against their upstream source on the updated date and course instructions are statically validated. A blank last_full_smoke_test means the complete GPU workflow has not been rerun by a course maintainer and must not be described as tested.",
  "tools": [
    {
      "id": "localcolabfold",
      "name": "LocalColabFold installer",
      "lesson": "monday/2-localcolabfold.qmd",
      "source": "https://github.com/YoshitakaMo/localcolabfold",
      "pin_kind": "git_commit",
      "pin": "e2e8c4a834a3d50ebaede3bb42786707fdc8f6ec",
      "installer_sha256": "4d97ec29fe5375171516869cda80fb814636f96115728a1735c9cf6fb5f979c8",
      "python": "managed by pinned installer",
      "accelerator": "CUDA GPU recommended",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "ligandmpnn",
      "name": "LigandMPNN",
      "lesson": "monday/3-ligandmpnn.qmd",
      "source": "https://github.com/dauparas/LigandMPNN",
      "pin_kind": "git_commit",
      "pin": "26ec57ac976ade5379920dbd43c7f97a91cf82de",
      "python": "3.11",
      "accelerator": "CPU or CUDA 12.1 wheels from pinned requirements",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "rfdiffusion2",
      "name": "RFdiffusion2",
      "lesson": "monday/4-rfdiffusion2.qmd",
      "source": "https://github.com/RosettaCommons/RFdiffusion2",
      "pin_kind": "git_commit",
      "pin": "d365cbf4db3958814a9f8e4f6f94fa309dfebc2b",
      "python": "inside upstream container",
      "accelerator": "CUDA GPU through Apptainer",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "esmfold",
      "name": "ESMFold",
      "lesson": "monday/5-esmfold.qmd",
      "source": "https://github.com/facebookresearch/esm",
      "pin_kind": "package_plus_git_commits",
      "pin": "fair-esm==2.0.0; OpenFold 4b41059694619831a7db195b7e0988fc4ff3a307; dllogger 0478734ff7be75adde8d160e04872664d1c62e5f",
      "python": "3.9",
      "accelerator": "CUDA GPU recommended",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "openfold",
      "name": "OpenFold",
      "lesson": "monday/6-openfold.qmd",
      "source": "https://github.com/aqlaboratory/openfold",
      "pin_kind": "git_commit",
      "pin": "be2ec1841f16c966c65ae0e7599ebbadc725757d",
      "python": "3.10 in pinned environment file",
      "accelerator": "PyTorch 2.5 / CUDA 12.4 in pinned environment file",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "chai1",
      "name": "Chai-1",
      "lesson": "monday/7-chai1.qmd",
      "source": "https://pypi.org/project/chai-lab/0.6.1/",
      "pin_kind": "python_package",
      "pin": "chai_lab==0.6.1",
      "source_commit": "8d5ac0f93e9b6ea4c3a6545c253a6381c0f3694b",
      "python": "3.11",
      "accelerator": "CUDA GPU with bfloat16 support recommended",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "boltz2",
      "name": "Boltz-2",
      "lesson": "monday/8-boltz2.qmd",
      "source": "https://pypi.org/project/boltz/2.2.1/",
      "pin_kind": "python_package",
      "pin": "boltz==2.2.1",
      "source_commit": "cb04aeccdd480fd4db707f0bbafde538397fa2ac",
      "python": "3.11",
      "accelerator": "CUDA GPU recommended; CPU supported",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "diffdock-pp",
      "name": "DiffDock-PP",
      "lesson": "monday/9-diffdock-pp.qmd",
      "source": "https://github.com/ketatam/DiffDock-PP",
      "pin_kind": "git_commit",
      "pin": "25a28900736c0730821e45265ee8e409751c358a",
      "python": "3.9",
      "accelerator": "PyTorch 1.13.0 / CUDA 11.6 course environment",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "placer",
      "name": "PLACER",
      "lesson": "monday/10-placer.qmd",
      "source": "https://github.com/baker-laboratory/PLACER",
      "pin_kind": "git_commit",
      "pin": "7dc5563300e7143582d85636bdd413d4c7688e9a",
      "python": "upstream pinned environment",
      "accelerator": "CPU or CUDA GPU",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "bindcraft",
      "name": "BindCraft",
      "lesson": "monday/11-bindcraft.qmd",
      "source": "https://github.com/martinpacesa/BindCraft",
      "pin_kind": "git_commit",
      "pin": "efb5bfeb8b4b1a5944256f979c34e0c8e6a82d9d",
      "python": "managed by pinned installer",
      "accelerator": "CUDA GPU with 24+ GB VRAM",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "esm3",
      "name": "ESM3",
      "lesson": "monday/12-esm3.qmd",
      "source": "https://pypi.org/project/esm/3.2.1.post1/",
      "pin_kind": "python_package",
      "pin": "esm==3.2.1.post1",
      "python": "3.10",
      "accelerator": "16+ GB CUDA GPU for esm3-small",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "rfdiffusion-aa",
      "name": "RFdiffusion All Atom",
      "lesson": "monday/13-rfdiffusion-aa.qmd",
      "source": "https://github.com/baker-laboratory/rf_diffusion_all_atom",
      "pin_kind": "git_commit",
      "pin": "f913a19e16f30858ce7a724fe028475b1871319c",
      "python": "inside upstream container",
      "accelerator": "CUDA GPU through Apptainer",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    },
    {
      "id": "rfdiffusion-original",
      "name": "Original RFdiffusion",
      "lesson": "wednesday/1-rfdiffusion.qmd",
      "source": "https://github.com/RosettaCommons/RFdiffusion",
      "pin_kind": "git_commit",
      "pin": "86507b6538f51fce57b5a72477165f03999ed7ae",
      "python": "upstream SE3nv environment",
      "accelerator": "CUDA 11.1-era environment; official outputs support no-compute study",
      "last_pin_review": "2026-08-30",
      "last_full_smoke_test": null
    }
  ]
}
