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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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Alphafill usage #23

Closed lukab86 closed 1 year ago

lukab86 commented 1 year ago

Can you please write an example of usage case of alphafill with all necessary steps, how should it be used to determine ion positions in a protein structure created by AlphaFold? Also, how should alphafill.conf look like, and how big is the database that needs to be downloaded? Thank you in advance.

drlemmus commented 1 year ago

You need to get the pdb-redo databank that is close to 2 TB although you can leave out a lot of data to reduce the size. If you are looking for a quick solution, it's best to use the upload function on alphafill.eu

lukab86 commented 1 year ago

Thank you very much for the quick response. But in case of the local usage, can you please provide a real life example, how would I add metal ions to an AlphaFold PDB structure including the config file and a proper Alphafill command?

drlemmus commented 1 year ago

The Readme has a description of the commands to run. You can add the following to the config file:

pdb-fasta=/DATA/pdb-redo/others/pdbredo_seqdb.txt pdb-dir=/DATA/pdb-redo/ ligands=/DATA/af-ligands.cif pdb-id-list=/DATA/pdb-id-list.txt