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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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Where are the selection of chemical compounds stored? #28

Closed r-krishna closed 1 year ago

r-krishna commented 1 year ago

Hello, thank you for this great work!

In your paper, I noticed "The current collection of compounds to be transplanted consists of 2,694 entries. It is stored separate from the AlphaFill program to allow easy extension in future incarnations of the AlphaFill databank and is freely available."

Could you point me to where these are located?

Thank you!

huiwenke commented 1 year ago

https://alphafill.eu/compounds Maybe their detailed information is in /usr/local/share/libcifpp/components.cif? The file can be downloaded from ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz.

mhekkel commented 1 year ago

The set of transplantable ligands is recorded in the file af-ligands.cif. You can find the default one here:

https://github.com/PDB-REDO/alphafill/blob/trunk/af-ligands.cif

If you build the software yourself, you can specify this file using a command line switch.