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.
What format do you have your peptide sequences in? I would assume they are in a String column as standard single-letter codes?
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.
Sounds great! thanks! waiting for updates…