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
Is your feature request related to a problem? Please describe.
The PDB is going to run out of 3 letter codes by the end of 2023 (see announcements 1, 2). This means that more and more PDB entries won't be available in legacy PDB format, adding to the growing list of reasons entries don't have a PDB file.
Describe the solution you'd like
Of course one can implement workaround (as I did previously for large structures).
But really, the long term, sustainable solution is support for mmCIF format as input.
In addition, this would mean such entries are available with the web tools (see for instance 4V9O, which cannot be analyzed currently).
Describe alternatives you've considered
Of course I could do some pre-processing of structures and rename 5-letter-code ligands to some of the reserved 3 letter codes (DRG, LIG, INH) and hope for the best.
But to be fair I'd rather not implement more and more workarounds. I don't think there are any long term alternative to mmCIF support.
xrobin
commented
8 months ago
Is your feature request related to a problem? Please describe. The PDB is going to run out of 3 letter codes by the end of 2023 (see announcements 1, 2). This means that more and more PDB entries won't be available in legacy PDB format, adding to the growing list of reasons entries don't have a PDB file.
Describe the solution you'd like Of course one can implement workaround (as I did previously for large structures). But really, the long term, sustainable solution is support for mmCIF format as input. In addition, this would mean such entries are available with the web tools (see for instance 4V9O, which cannot be analyzed currently).
Describe alternatives you've considered Of course I could do some pre-processing of structures and rename 5-letter-code ligands to some of the reserved 3 letter codes (DRG, LIG, INH) and hope for the best. But to be fair I'd rather not implement more and more workarounds. I don't think there are any long term alternative to mmCIF support.
Additional context No