Commits · e93a9eb64fb33b875ed0c6bef5f19089f66e0e5a · ModelZoo / alphafold2_jax

"router/src/infer/v2/queue.rs" did not exist on "b6ee0ec7b06b11ad35fe2f2d99318ddc47f95558"

28 Jan, 2022 1 commit
- Explain what to do if downloading PDB mmCIF files is too slow. · e93a9eb6
  Augustin Zidek authored Jan 28, 2022
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27 Jan, 2022 1 commit
- Release code for v2.1.2 · 57a2455e
  Augustin Zidek authored Jan 27, 2022
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  57a2455e
19 Jan, 2022 2 commits
- Update .dockerignore · db039ef4
  Tim Green authored Jan 19, 2022
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Don't ignore the README.md.
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  db039ef4
- Update license of AlphaFold parameters. · 81731171
  Augustin-Zidek authored Jan 19, 2022
  
  81731171
05 Nov, 2021 2 commits

Explain better how to run the AlphaFold-Multimer system. · be37a41d

Augustin Zidek authored Nov 05, 2021

* Remove a confusing example that folds multiple complexes at once.
* Add examples on how to create the multimer input FASTA files.
* Add a note about the `model_preset` flag to the API changes.

PiperOrigin-RevId: 407774039
Change-Id: I80277c47febc977ba3956d0615944e62b0d5c3fc

be37a41d

Fix PAE visualization for single chain predictions. · 91b43223
Rich Evans authored Nov 05, 2021
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04 Nov, 2021 1 commit
- Change fasta description used in data pipeline to be chain_<chain number>. · c128d1aa
  Andrew Cowie authored Nov 04, 2021
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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.

PiperOrigin-RevId: 395878875
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

PiperOrigin-RevId: 394105499
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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- Use pLDDT in the B-factor column of the output PDBs. · cef198e0
  Augustin Zidek authored Aug 13, 2021
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PiperOrigin-RevId: 390566020
Change-Id: I3fafbe8246d0a5ad018f0398b39bf7dacee00468
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- Set versions of libraries AlphaFold Colab notebook depends on. · f65e94fc
  Augustin Zidek authored Aug 13, 2021
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PiperOrigin-RevId: 390553964
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12 Aug, 2021 1 commit

Remove a redundant space. · 05db248e

Augustin Zidek authored Aug 12, 2021

PiperOrigin-RevId: 390355132
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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PiperOrigin-RevId: 388195957
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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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- Use Ubuntu 18.04 LTS image. · c9ffb0bc
  Tim Green authored Jul 30, 2021
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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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- Change tex -> bibtex for nicer syntax highlighting. · bc5547b6
  Augustin Zidek authored Jul 29, 2021
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PiperOrigin-RevId: 387546070
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27 Jul, 2021 3 commits
- Fix import ordering. · 1e216f93
  Tom Ward authored Jul 27, 2021
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PiperOrigin-RevId: 387085679
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- Collapse hh-suite install steps into single layer. · c9e6fedb
  Tom Ward authored Jul 27, 2021
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PiperOrigin-RevId: 387060806
Change-Id: Ifa71ce119182ed79a379e57946b2b694e134ef14
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- Switch to using cudnn base image. · acf25fc8
  DeepMind authored Jul 27, 2021
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PiperOrigin-RevId: 387058301
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26 Jul, 2021 2 commits
- Write out pdb70_hits.hhr alongside other MSA outputs. · 2028cd0a
  DeepMind authored Jul 26, 2021
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Change-Id: I1ef2018a48398cf8201ac38fe129b004672ad22f
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- Correct mgnify clusters filename. · 20a70577
  DeepMind authored Jul 26, 2021
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23 Jul, 2021 1 commit

Fix a link in the README · d3a4eefd

DeepMind authored Jul 23, 2021

PiperOrigin-RevId: 386417647
Change-Id: I6f2121f3c02d3ef97467f46c5e651ca1b0f2eab2

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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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