Hi,
What’s the best way to read sequences of short peptides and convert them to SMILES(?) to further calculate descriptors?
I tried to upload a FASTA file and use openbabel for conversion, but it interprets the fasta sequence as nucleotides, not amino acids.
Tnx
What format do you have your peptide sequences in? I would assume they are in a String column as standard single-letter codes?
Steve
Yes, strings of single-letter codes
OK, so we have an internal node which will do exactly this. You can choose ‘alphabet’ type (Protein, DNA, RNA etc), and the node will output a SMILES string. As it does not rely on any toolkits and therefore has no library loading or format conversion overheads, it is reasonably fast too.
I have just requested formal permission to release the node. Assuming no objections are raised, then that should be possible within the next few days.
Steve
Sounds great! thanks! waiting for updates…
The nodes have just been release - see Update to v1.35.0 - New 'Speedy Sequence' nodes and PDB Connector Query Builder Bug Fix for details
Steve