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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
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Running AlphaFill locally on one's own AlphaFold models #13

Closed eric-jm-lang closed 1 year ago

eric-jm-lang commented 1 year ago

Hello,

Thank you for this very interesting tool.

Something is not clear to me: if I install AlphaFill locally (along with PDB-REDO or PDB in mmCIF format and the associated fasta file), can I then use it to transplant co-factors and ions on my own AlphaFold models (i.e. without any Uniprot ID)?

If so, what sort of command should I run? I am not sure to understand what the alphafill /srv/data/afdb/cif/AF-XXX.cif.gz /srv/data/af-filled/AF-XXX.cif.gz command do.

Many thanks in advance for your help.

mhekkel commented 1 year ago

Sssh, don't tell anyone, but you can now upload your own sequences to https://alphafill.eu/test/

That upload feature will be publicly available soon.

But to answer your question, yes, you can build and run alphafill locally. The example command you quote is taking an input file and output file as parameters. The rest of the options are inside a config file.

You can run alphafill --help to see what the other options are.