Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
I've been using Python PLIP to detect interactions between a protein and a peptide, and I noticed that it seems to be missing halogen bonds.
Upon checking the function in plip.structure.detection.halogen, I saw the code and its comment: "Detect all halogen bonds of the type Y-O...X-C".
My question is, why does this function only focus on Y-O bonds, even though there are other possible formats like Y-{O|P|N|S} (as mentioned in the find_hal method)?
UPDATE:
Probably find_hal in BindingSite is wrong?
The definition of halogen acceptor in your document is 'Halogen bond acceptors in proteins are all carbon, phosphor or sulphur atoms connected to oxygen, phosphor, nitrogen or sulfur.', but in the code, you used 'All oxygens, nitrogen, sulfurs with neighboring carbon, phosphor, nitrogen or sulfur'.
Hi PLIP Team,
I've been using Python PLIP to detect interactions between a protein and a peptide, and I noticed that it seems to be missing halogen bonds.
Upon checking the function in plip.structure.detection.halogen, I saw the code and its comment: "Detect all halogen bonds of the type Y-O...X-C".
My question is, why does this function only focus on Y-O bonds, even though there are other possible formats like Y-{O|P|N|S} (as mentioned in the find_hal method)?
UPDATE: Probably find_hal in BindingSite is wrong? The definition of halogen acceptor in your document is 'Halogen bond acceptors in proteins are all carbon, phosphor or sulphur atoms connected to oxygen, phosphor, nitrogen or sulfur.', but in the code, you used 'All oxygens, nitrogen, sulfurs with neighboring carbon, phosphor, nitrogen or sulfur'.
Thank you for your patience!