We are excited to present our latest release - OpenBind v0!!
This release comes with a new set of parameters: openbind-2025-06-03-174k (filename of3-ob-2025-06-30-174k.pt)
If you already have an installation of openfold3, please rerun setup_openfold to ensure that your installation has the latest model parameters. Also note that the previously released preview 2 weights are deprecated and will not function correctly with openfold3>=0.5. Instructions on how to use the preview 2 release can be found here.
The key changes in the OpenBind release from the preview 2 release are:
Training schedule changes
- Moved the pair layer norm in the diffusion transformer out of attention pair bias. The pair layer norm is run once to match the AlphaFold3 SI.
- Restricted the spatial crop center atom on sampled interfaces to the actual interface region, instead of anywhere within the two chains.
- Full support for training on AMD chips
Bug fixes
- MSA profile column index scrambling (as reported in #312)
- Deletion values scaled by a factor of four during featurization
- MSA pairing logic not pairing correctly
- Stale residue offsets causing templates to be dropped without warning
- MSA truncation not applying the configured depth limit (as reported in #308)
Changes to come in upcoming releases
- RNA frame definition fix (reported here: #247)
What's Changed
- automatically load user-default runner.yml from cache directory by @CesarPuentes in #358
- docs: remove erroneous ccd_file_path from query.json example by @Vincy1230 in #370
- Fixing online MSA pairing - inference by @jnwei in #373
- OpenBind model release by @jnwei in #375
New Contributors
- @Vincy1230 made their first contribution in #370
Full Changelog: 0.4.5...v0.5.0
Contributors
Vincy1230, jnwei, and CesarPuentes