Can I add new PDB templates

[rajanprabu]

Hi alphafold team,

Thanks for releasing the code for academic use. I have a small question regarding the templates that AF uses. We want to use some structures that was released last weeks and it's not yet there in the mmciif templates that AF uses ( it was dated to pdb_2022_09_28). My question can I simply drop the new mmcif files within that folder and AF can use that ?

Also is the database date same as 2022_09_28 the public alphfolder server ?

Thanks for your time and effort.

[Augustin-Zidek]

Hi,

you have two options:

Option 1: Update to the newest version of PDB

1. Put the new mmCIF files in the mmcif_files/ directory).
2. Update the PDB seqres FASTA file to match the version of the mmCIF files. Otherwise Hmmsearch will never find the template sequence and fetch the mmCIF file for it.
3. Update PDB seqres path using the --seqres_database_path flag.

Option 2: Use custom templates

You could manually craft the input JSON to contain the desired MSA and template(s). See https://github.com/google-deepmind/alphafold3/blob/main/docs/input.md#structural-templates for instructions. However, this is a bit fiddly, so I recommend going for option 1.

Also is the database date same as 2022_09_28 the public alphfolder server ?

Yes, the default settings and db versions match AlphaFold Server and the AlphaFold 3 paper.