Commits · 0be2b30b98f0da7aecb973bde04758fae67eb913 · ModelZoo / alphafold2_jax

02 Nov, 2021 1 commit
- Add code for AlphaFold-Multimer. · 0be2b30b
  Augustin-Zidek authored Nov 02, 2021
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  0be2b30b
10 Sep, 2021 2 commits

Accept any ordering given by ListDir in the assert. · 1d43aaff

Augustin Zidek authored Sep 10, 2021

Addresses https://github.com/deepmind/alphafold/issues/168.

PiperOrigin-RevId: 395907797
Change-Id: I28c7e951211c9cf6bd5e35d8dfaf57f22e843ed0

1d43aaff

Skip obsolete PDB templates that don't have a replacement. · 50ecd75d

Augustin Zidek authored Sep 10, 2021

Fixes https://github.com/deepmind/alphafold/issues/163.

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Change-Id: I99a9defa95547582bbfd9fec3ae821386274d77f

50ecd75d

31 Aug, 2021 2 commits

Ensure values passed to jax.numpy functions are arrays rather than lists. · 98caef21

Jake VanderPlas authored Aug 31, 2021

Why? This will soon be a requirement in JAX; see https://github.com/google/jax/issues/7737

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Change-Id: I6f76e3f47b7906616c1f988be58d29c828414060

98caef21

Update the bibtex citation with the issue number and pages · 495d81ac
Michael Figurnov authored Aug 31, 2021
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495d81ac

25 Aug, 2021 1 commit
- Fix TensorFlow versions in AlphaFold Colab notebook. · b1d772d1
  DeepMind authored Aug 25, 2021
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13 Aug, 2021 3 commits
- Use tensorflow-cpu in setup.py as well. · 99459eff
  Augustin Zidek authored Aug 13, 2021
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  99459eff
- Use pLDDT in the B-factor column of the output PDBs. · cef198e0
  Augustin Zidek authored Aug 13, 2021
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  cef198e0
- Set versions of libraries AlphaFold Colab notebook depends on. · f65e94fc
  Augustin Zidek authored Aug 13, 2021
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  f65e94fc
12 Aug, 2021 1 commit

Remove a redundant space. · 05db248e

Augustin Zidek authored Aug 12, 2021

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Change-Id: I920a80db674541af41ee83ef3d5bd5255c782ee9

05db248e

02 Aug, 2021 2 commits

Add a direct link to PDB70 2020-05-13. · 547cbddb
Augustin Zidek authored Aug 02, 2021
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547cbddb

Fix a few typos. · 41232dc7

Augustin Zidek authored Aug 02, 2021

PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab

41232dc7

30 Jul, 2021 2 commits
- Add a comment on the TriangleMultiplication notation. · b88f8dac
  DeepMind authored Jul 30, 2021
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  b88f8dac
- Use Ubuntu 18.04 LTS image. · c9ffb0bc
  Tim Green authored Jul 30, 2021
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  c9ffb0bc
29 Jul, 2021 3 commits
- Log the total MSA size and number of templates. · 00c4c91d
  Alex Bridgland authored Jul 29, 2021
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- Switch to Tensorflow CPU-only. GPU not needed for data pipeline. · b3ed8603
  Tim Green authored Jul 29, 2021
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  b3ed8603
- Change tex -> bibtex for nicer syntax highlighting. · bc5547b6
  Augustin Zidek authored Jul 29, 2021
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  bc5547b6
27 Jul, 2021 3 commits
- Fix import ordering. · 1e216f93
  Tom Ward authored Jul 27, 2021
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  1e216f93
- Collapse hh-suite install steps into single layer. · c9e6fedb
  Tom Ward authored Jul 27, 2021
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  c9e6fedb
- Switch to using cudnn base image. · acf25fc8
  DeepMind authored Jul 27, 2021
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  acf25fc8
26 Jul, 2021 2 commits
- Write out pdb70_hits.hhr alongside other MSA outputs. · 2028cd0a
  DeepMind authored Jul 26, 2021
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  2028cd0a
- Correct mgnify clusters filename. · 20a70577
  DeepMind authored Jul 26, 2021
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  20a70577
23 Jul, 2021 1 commit

Fix a link in the README · d3a4eefd

DeepMind authored Jul 23, 2021

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d3a4eefd

22 Jul, 2021 1 commit
- Add a Colab notebook, add reduced BFD, and various other fixes and improvements. · 0bab1bf8
  Saran Tunyasuvunakool authored Jul 22, 2021
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  0bab1bf8
16 Jul, 2021 1 commit
- Switch BFD download script to mirror. · d26287ea
  Tim Green authored Jul 16, 2021
  
  d26287ea
15 Jul, 2021 1 commit
- Initial release of AlphaFold. · 1109480e
  Augustin-Zidek authored Jul 15, 2021
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  1109480e