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AlphaFold v2.2.0

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@Augustin-Zidek Augustin-Zidek released this 10 Mar 15:38
· 95 commits to main since this release

Version v2.2.0 updates the AlphaFold-Multimer model parameters. These new models have greatly reduced numbers of clashes on average and are slightly more accurate. Read the updated AlphaFold-Multimer paper for more details.

A number of other bug fixes and small improvements have been made.

Change log

  • Added new AlphaFold-Multimer models with greatly reduced numbers of clashes on average and slightly increased accuracy.
  • Use DeviceRequest rather than runtime=nvidia to expose GPUs to the container (thanks @aburger).
  • Simplified mounting of files in Docker.
  • Removed unused bias argument in GlobalAttention (thanks @breadbread1984).
  • Removed prokaryotic MSA pairing algorithm as it didn’t improve accuracy on average.
  • Added the ability to run with multiple seeds per model to match the AlphaFold-Multimer paper.
  • Fixed degraded performance when using num_recycle=0 with models trained with recycling due to incorrect skipping of layers (thanks @sokrypton).
  • Added split_rng=False (current default) to sharded_map to support new Haiku release.
  • Removed unused code in amber_minimize.py.