google-deepmind/alphafold3 v3.0.3

AlphaFold v3.0.3

Repository: google-deepmind/alphafold3

Tag: v3.0.3

Published: 2026-06-09T12:26:50Z

Prerelease: no

Release notes: Version 3.0.3 changes the AlphaFold 3 code license from CC BY-NC-SA 4.0 to Apache 2.0. Moreover, it provides bug fixes and a performance improvement for large inputs. We thank everyone who reported issues, proposed new features, and submitted PRs!

Change log

Below is a selection of new features, performance improvements and bug fixes. Full change log: v3.0.2...v3.0.3

New features

• AlphaFold 3 is now compatible with Python 3.14.
• The AlphaFold 3 code is now relicensed from CC BY-NC-SA 4.0 to Apache 2.0.

Performance improvements

• Confidences JSON serialization is up to 30x faster, for a 5,000-residue input the serialization time drops 43 -> 1.3 s.
• mmCIF parsing is 4% faster.

Bug fixes

• A new flag was introduced to not drop O1 atom from non-linking saccharides/glycans. Thanks @magnusbauer and @Jonas-Wilhelm.
• Added support for dynamic version (inferred from the commit history) for dev and releases. Thanks @ccoulombe.
• Pass all flags correctly to Jackhmmer/Nhmmer. Thanks @chenbq18.
• Fix glycan O1 leaving-atom cleanup for standalone glycans. Thanks @Jonas-Wilhelm and @magnusbauer.
• Do not drop chain descriptions for RNA and protein chains. Thanks @ntnn19.
• Fixes of typing issues revealed by Pyrefly.

Documentation

• Fixed typos in docstrings, thanks @mooreneural.

We thank the following people for their pull requests and/or great suggestions: @ccoulombe, @Jonas-Wilhelm, @magnusbauer, @mooreneural, @ntnn19.