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OpenFold3 Preview2 Release

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@jnwei jnwei released this 13 Mar 11:46
· 11 commits to main since this release
0.4.0
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Learn about vigilant mode.

The OpenFold team is excited to announce the release of OpenFold3 preview 2! 🎉🎉

  • We release a new model that exhibits significant improvement on small molecules and biologics. This model also exhibits inference time scaling for antibody structure predictions. See our whitepaper for full results

  • We release the datasets used to train the OpenFold3 models, containing >10M datapoints! See https://portal.openfold.omsf.io/datasets for more info

  • OpenFold3 is now fully packaged on pypi and easier to install than ever! To install openfold3, all you need is:

pip install openfold3

Special thanks to @TimoLassman and @etowahadams for building and packaging python-kalign to enable this change

Breaking changes:

  • Model parameters from OF3p (e.g. of3_ft3_v1.pt are not compatible with openfold3 versions after this release e.g. >=0.4.0)

  • The command setup_openfold will no longer create an $OPENFOLD_CACHE environment variable. Users who wish to set up a custom cache path should set the OPENFOLD_CACHE variable separately

Significant changes:

  • Template alignments: OpenFold3 has updated to use kalign3 available from [kalign-python](https://pypi.org/project/kalign-python/) on pypi instead of kalign2. All kalign alignments now use the python API. There should be no effect on downstream usage of OpenFold3.

What's Changed

  • Feature/update docs by @ljarosch in #10
  • add benchmarks and rename imgs to assets by @vinay-swamy in #11
  • fix: make test root directory where install is by @etowahadams in #12
  • Move up documentation section by @ljarosch in #18
  • create DOI for repo by @vinay-swamy in #19
  • Fix formatting and update YAML instructions in kernels.md by @jnwei in #20
  • Fix presets field in ModelUpdate by @jnwei in #24
  • Add Blackwell GPU support using NVIDIA PyTorch container by @eidamo in #26
  • Add a Pull Request Template by @jnwei in #29
  • Support dummy sequence MSA by @haewonc in #28
  • Docker image publishing and change CI infrastructure by @jnwei in #48
  • Fix: Handle empty pdb70.m8 template file from ColabFold by @qurat-ul-ain95 in #38
  • Amend cutlass hacks to support docker image by @jnwei in #49
  • Bump docker/build-push-action from 4.0.0 to 6.18.0 by @jnwei in #65
  • Update CI test configuration by @jnwei in #67
  • Fix sample ranking formula by @qurat-ul-ain95 in #59
  • feat(config): Add optional 'description' field to Chain input (#57) by @chodec in #64
  • Fix Quick-Start Guide Command by @gloriamacia in #68
  • Update DOI in README.md by @maabuu in #74
  • build(docker): layering and caching improvements by @jandom in #70
  • build: added environment.lock for 'stable' builds by @jandom in #75
  • refactor: download_of3_databases.py and add tests by @jandom in #77
  • build: remove setup.py and other build changes by @jandom in #79
  • fix: typo in Dockerfile by @jandom in #83
  • fix: missing import in preprocess_pdb_of3 by @jandom in #86
  • refactor: tests for the cleanup.py by @jandom in #87
  • feat: adding pytest-cov and pytest-xdist by @jandom in #90
  • refactor: dummy_atom_array by @jandom in #88
  • refactor: tests for cleanup.py by @jandom in #89
  • fix: pytest-cov and pytest-xdist were put under 'dev' instead of 'test' by @jandom in #92
  • fix: preparse_alignments_of3 and add tests by @jandom in #81
  • fix: explicit hydrogens inference issue by @ljarosch in #98
  • tweak: include .coverage by @jandom in #99
  • feat: docker image for SandboxAQ/aqaffinity by @jandom in #102
  • test: get_pairing_masks by @jandom in #100
  • fix: CCD/SMILES inconsistency by @jandom in #95
  • docs: how to get model embeddings (s_i, z_ij) by @jandom in #105
  • fix: missing AWS credentials in GHA by @jandom in #106
  • Add grouping for dependabot PRs by @jnwei in #107
  • Bump omsf/start-aws-gha-runner from 1.1.0 to 1.1.1 by @dependabot[bot] in #76
  • chore(deps): bump the github-actions group with 3 updates by @dependabot[bot] in #108
  • Update Dockerfile to install openfold3 for aqaffinity by @brianloyal in #112
  • fix: .coverage file missing from the GHA artifact by @jandom in #113
  • docs: debugging instructions for docker by @jandom in #114
  • docs: improve pytest-cov configuration by @jandom in #116
  • fix: setup CCD not actually downloading anything by @jandom in #118
  • chore(deps): bump aws-actions/configure-aws-credentials from 5 to 6 in the github-actions group by @dependabot[bot] in #123
  • build: harmonize docker image pushes by @jandom in #126
  • ci: require the safe-to-test label only on the public repo by @jandom in #125
  • fix: small fixes used when finetuning a model by @avelinoapheris in #45
  • chore: move update_ccd.py to scripts/dev by @jandom in #129
  • feat: enable cuequivariance kernels on the base image by @avelinoapheris in #44
  • chore(deps): bump the github-actions group with 2 updates by @dependabot[bot] in #131
  • Fix tokenization bug based on invalid sym_id assignment for unresolved atoms by @jnwei in #124

New Contributors

Full Changelog: 0.3.1...0.4.0

Contributors

jandom, etowahadams, and 12 other contributors
Assets 2
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