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Releases: google-deepmind/alphafold

AlphaFold v2.1.0

02 Nov 17:14
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Version 2.1.0 adds the AlphaFold-Multimer model and fixes a number of issues reported in the last few months.

Change log:

  • [new feature] AlphaFold-Multimer data pipeline, model and metrics have been added. Use model_preset=multimer to run with AlphaFold-Multimer.
  • [change] AlphaFold-Multimer no longer pre-processes the features via TensorFlow but instead does it in the JAX module code.
  • Added a note and a check that the directory with data is outside the AlphaFold repository for faster Docker builds (thanks @jamespeapen).
  • Advertise Python 3.7, 3.8, 3.9, 3.10 in setup.py (thanks @anukaal).
  • Added an FAQ explaining that the Colab on free tier can time out (thanks @mooingcat).
  • Stop using hardcoded /tmp, instead use $TMPDIR (thanks @meson800, @EricDeveaud).
  • Make run_docker fully configurable via flags: data_dir, docker_image_name, output_dir (thanks @akors, @chrisroat).
  • Look for stereo_chemical_props.txt relative to the residue_constants module (thanks @rjgildea).
  • Crop UniRef90 MSA to 10,000 sequences to prevent hitting the 2 GB proto field limit and use less memory (thanks @biohegedus and @chrisroat).
  • Finding third party tool binaries is now more robust and gives you better errors if any are missing (thanks @FanchTheSystem).
  • Refactor and a few fixes and usability improvements in the AlphaFold Colab.

AlphaFold v2.0.1

30 Sep 10:40
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Version 2.0.1 is mainly a bug fix release. We thank everyone who reported issues and proposed solutions.

Change log:

  • [new feature] Added AlphaFold Colab notebook that enables convenient folding from your browser.
  • [new feature] The reduced_dbs preset was added together with small BFD.
  • Some of the genetic databases are now mirrored on GCP.
  • Added a missing data/__init__.py and model/tf/__init__.py files.
  • README fixes and additions.
  • Switched to using cudnn base image based on Ubuntu 18.04.
  • Switched to tensorflow-cpu since we don't need a GPU when running the data pipeline.
  • Improved logging in the AlphaFold pipeline.
  • Fixed a few typos and added and fixed a few comments.
  • Added pLDDT in the B-factor column of the output PDBs.
  • Skip obsolete PDB templates that don't have a replacement.
  • Small test improvements.

Initial release

16 Jul 14:58
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Initial release of AlphaFold.

PiperOrigin-RevId: 384954738