Open taywpd opened 1 year ago
Hello Dillon,
Thank you for your insterest in RNAmigos.
This is always the trickiest part of the whole thing.
First, I assume that by secondary structure you mean tertiary structure since for this to work you need to have 3D coordinates of the RNA and not just the secondary structure (canonical base pairs).
It all depends on whether or not the RNA you are using is in the RCSB PDB Databank or not.
Case 1.: In the PDB Databank
Case 2: Not in the PDB Databank
tldr; it's easy if your RNA is available in the PDB, if not, there is some work to do but it's not impossible. In both cases, I'm happy to help.
Best, Carlos
Dear Dr. Oliver,
Thank you for the very nice program. I was wondering:
Assuming we have a predetermined small secondary RNA structure we want to designate as the binding pocket, is there a way to convert 3D coordinates of that RNA secondary structures into the NetworkX graph input required by the RNAmigos model?
Cheers, Dillon