Good morning ;)
I knew interesting method ‘MolFromSequence’ in RDKit UGM2020. It can build molecule object from amino acid sequences. It means that I can get mol object from amino acid sequence such as ‘GGGG’ ;).
And recently, macro molecule is the one of interesting strategy for drug discovery. So I would like to test how to build macro cyclic peptide with rdkit. The code is really simple, only two steps. 1) define rxn of intra-molecular cyclization 2) define peptide of target, 3) run rxn! The image is below.
My rxn definition is not perfect but following example worked well. It is easy to define more efficient query depends on user situation I think. Recent version of rdkit can Render macrocyclic compounds with good 2D coordinations.
Now current MolFromSequence supports only peptides. But user can add some flavor when user constructs molecules. Details are described following URL.
And my code is found on my gist.
And more.
You can get many useful information from UGM repo https://github.com/rdkit/UGM_2020. Don’t miss it!
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