important homologs seem to be missing

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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important homologs seem to be missing #6

Closed esbenfriis closed 2 years ago

esbenfriis commented 2 years ago

Really great tool!

I noticed that alphafill does not always pick up all relevant entries with ligands in the PDB. For example, AF-P0DUB9-F1 should find 4LIP and 5LIP which are about 84% identical to P0DUB9 and have relevant ligands.

drlemmus commented 2 years ago

AlphaFill uses the PDB-REDO databank which in turn only uses PDB entries that have experimental data. 4lip and 5lip do not have such data. If you can convince the PDB depositors to deposit their experimental data, we are happy to make sure the ligands are transferred.