google-deepmind / google-deepmind/alphafold
Should PDB70 version be incremented in Alphafold version 2.3.1?
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Description
The README section on [CASP14 reproducibility with version 2.3.1](https://github.com/deepmind/alphafold#note-on-casp14-reproducibility) implies that one should use old versions of the databases (and gives versions), or using current PDB70 and PDB but passing the `--max_template_date` command line flag to reproduce the CASP14 results. The dates for the (implied older) versions of the databases for PDB and PDB70 are 2020-05-13.
The version of the PDB70 downloaded by the scripts is `pdb70_from_mmcif_200401.tar.gz` (2020-04-01). This has been the version downloaded by the script since the [initial commit of the repo](https://github.com/deepmind/alphafold/blob/main/scripts/download_pdb70.sh#L34).
Is this a bug? Should a more recent version be used and set as the default in the download scripts?
Dates for readily available versions of the PDB70 are as follows
- 2020-04-01 (version currently hard coded in the download script)
- 2020-05-13 (version recommended in README for reproducing CASP14 results)
- 2020-09-16
- 2021-10-27
- 2021-11-17
- 2022-03-13
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