Include a ligand in the structure

[jhrcook]

Thank you for putting this repo together, it is really helpful in understanding and preparing the features for AlphaFold. I was wondering if it is possible to include non-covalently-linked ligands alongside the amino acids in the protein. For instance, could I include a small-molecule substrate for an enzyme? If this is possible, can you explain how I could do this?

[mpds]

Have you tried protein-ligand docking? There are web portals available, such as this one.

[jhrcook]

For my use case, I know where the ligand will go, I'm just not sure how to include it in the FASTA to be used in the model's prediction.