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Author SHA1 Message Date
Tim Green
db039ef423 Update .dockerignore 
Don't ignore the README.md.
 2022-01-19 21:39:18 +00:00
Augustin-Zidek
8173117130 Update license of AlphaFold parameters. 2022-01-19 14:58:43 +00:00
Augustin Zidek
be37a41d6f Explain better how to run the AlphaFold-Multimer system. 
* 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
v2.1.1 		2021-11-05 02:38:51 -07:00
Rich Evans
91b4322342 Fix PAE visualization for single chain predictions. 
PiperOrigin-RevId: 407773747
Change-Id: I8635dd77ecf366f4f5a362993b964adffc3ff186
 2021-11-05 02:36:42 -07:00
Andrew Cowie
c128d1aa2c Change fasta description used in data pipeline to be chain_<chain number>. 
PiperOrigin-RevId: 407584472
Change-Id: Icfa755722ddabff71d27f4a3d07f9e88a409c3a6
 2021-11-04 08:21:49 -07:00
Augustin-Zidek
0be2b30b98 Add code for AlphaFold-Multimer. 
PiperOrigin-RevId: 407076987
v2.1.0 		2021-11-02 14:33:58 +00:00
Augustin Zidek
1d43aaff94 Accept any ordering given by ListDir in the assert. 
Addresses https://github.com/deepmind/alphafold/issues/168.

PiperOrigin-RevId: 395907797
Change-Id: I28c7e951211c9cf6bd5e35d8dfaf57f22e843ed0
v2.0.1 		2021-09-10 05:34:22 -07:00
Augustin Zidek
50ecd75dac Skip obsolete PDB templates that don't have a replacement. 
Fixes https://github.com/deepmind/alphafold/issues/163.

PiperOrigin-RevId: 395878875
Change-Id: I99a9defa95547582bbfd9fec3ae821386274d77f
 2021-09-10 01:45:04 -07:00
Jake VanderPlas
98caef21ef Ensure values passed to jax.numpy functions are arrays rather than lists. 
Why? This will soon be a requirement in JAX; see https://github.com/google/jax/issues/7737

PiperOrigin-RevId: 394105499
Change-Id: I6f76e3f47b7906616c1f988be58d29c828414060
 2021-08-31 16:03:05 -07:00
Michael Figurnov
495d81ac1f Update the bibtex citation with the issue number and pages 
PiperOrigin-RevId: 393964942
Change-Id: I9c45191f726b40b66cea1cdd9f2efa2d4082b084
 2021-08-31 04:24:38 -07:00
DeepMind
b1d772d127 Fix TensorFlow versions in AlphaFold Colab notebook. 
PiperOrigin-RevId: 392861510
Change-Id: I266255479210e5c9b6cbc02977f4024d40c5b94d
 2021-08-25 03:51:49 -07:00
Augustin Zidek
99459effce Use tensorflow-cpu in setup.py as well. 
PiperOrigin-RevId: 390608262
Change-Id: I4c49aeb2aea362d578b7de43d16bf2e418fdd96d
 2021-08-13 07:29:34 -07:00
Augustin Zidek
cef198e0b6 Use pLDDT in the B-factor column of the output PDBs. 
PiperOrigin-RevId: 390566020
Change-Id: I3fafbe8246d0a5ad018f0398b39bf7dacee00468
 2021-08-13 02:13:24 -07:00
Augustin Zidek
f65e94fc71 Set versions of libraries AlphaFold Colab notebook depends on. 
PiperOrigin-RevId: 390553964
Change-Id: Ia5bc6e12ab3f1a7827b7d914c93f6990a1139780
 2021-08-13 00:39:52 -07:00
Augustin Zidek
05db248e91 Remove a redundant space. 
PiperOrigin-RevId: 390355132
Change-Id: I920a80db674541af41ee83ef3d5bd5255c782ee9
 2021-08-12 06:27:04 -07:00
Augustin Zidek
547cbddbf1 Add a direct link to PDB70 2020-05-13. 
PiperOrigin-RevId: 388195957
Change-Id: Id22b96c964a82e3450a5f457d8facd1e85b1e86a
 2021-08-02 05:22:45 -07:00
Augustin Zidek
41232dc756 Fix a few typos. 
PiperOrigin-RevId: 388172326
Change-Id: I11d9e498c226cd752947feb51b7d1eb343b4d7ab
 2021-08-02 02:04:31 -07:00
DeepMind
b88f8dacef Add a comment on the TriangleMultiplication notation. 
PiperOrigin-RevId: 387766802
Change-Id: Ic838537513fe1d5bf41facffffd44046e91c3fa3
 2021-07-30 02:47:12 -07:00
Tim Green
c9ffb0bc18 Use Ubuntu 18.04 LTS image. 
PiperOrigin-RevId: 387763552
Change-Id: I2a9753dfca2853de7f5c07c17cc7b2f7d12cf197
 2021-07-30 02:20:00 -07:00
Alex Bridgland
00c4c91dcc Log the total MSA size and number of templates. 
PiperOrigin-RevId: 387577557
Change-Id: I37c0a748dd3d8d3d179aae579c5504d7ec92ecaf
 2021-07-29 07:16:10 -07:00
Tim Green
b3ed8603e8 Switch to Tensorflow CPU-only. GPU not needed for data pipeline. 
PiperOrigin-RevId: 387576219
Change-Id: Ic735f068df2a3e9f53bed836f172c08f79ac231c
 2021-07-29 07:07:05 -07:00
Augustin Zidek
bc5547b6c2 Change tex -> bibtex for nicer syntax highlighting. 
PiperOrigin-RevId: 387546070
Change-Id: I24cce3825801dde09be70970cf48141679762a2a
 2021-07-29 03:04:54 -07:00
Tom Ward
1e216f93f0 Fix import ordering. 
PiperOrigin-RevId: 387085679
Change-Id: I73287fcd0a29e899543b64c596e306195a2f435e
 2021-07-27 05:31:03 -07:00
Tom Ward
c9e6fedb6b Collapse hh-suite install steps into single layer. 
PiperOrigin-RevId: 387060806
Change-Id: Ifa71ce119182ed79a379e57946b2b694e134ef14
 2021-07-27 02:24:29 -07:00
DeepMind
acf25fc879 Switch to using cudnn base image. 
PiperOrigin-RevId: 387058301
Change-Id: If7d2716bfe89228e9fb8f909b72c425bd89f1f7f
 2021-07-27 02:04:57 -07:00
DeepMind
2028cd0a51 Write out pdb70_hits.hhr alongside other MSA outputs. 
PiperOrigin-RevId: 386894639
Change-Id: I1ef2018a48398cf8201ac38fe129b004672ad22f
 2021-07-26 09:41:18 -07:00
DeepMind
20a705778f Correct mgnify clusters filename. 
PiperOrigin-RevId: 386841647
Change-Id: Ie3ad390fc4b53b839f15c01f3b24bd25c77578b6
 2021-07-26 04:24:53 -07:00
DeepMind
d3a4eefdfc Fix a link in the README 
PiperOrigin-RevId: 386417647
Change-Id: I6f2121f3c02d3ef97467f46c5e651ca1b0f2eab2
 2021-07-23 02:55:24 -07:00
Saran Tunyasuvunakool
0bab1bf84d Add a Colab notebook, add reduced BFD, and various other fixes and improvements. 
PiperOrigin-RevId: 386228948
 2021-07-22 15:16:43 +01:00
Tim Green
d26287ea57 Switch BFD download script to mirror. 2021-07-16 23:11:24 +00:00
Augustin-Zidek
1109480e6f Initial release of AlphaFold. 
PiperOrigin-RevId: 384954738
v2.0.0 		2021-07-15 18:44:37 +01:00