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- September 23, 2020 at 2:56 pm #15905Andrey FrolovGuest
Dimorphite-DL seems to confuse the cyclic amides with amines. E.g. see the test molecule below. These substructures used in cross-linking peptides known as TATA or TATB cores (https://pubs.acs.org/doi/10.1021/acs.accounts.7b00184), so they are not very exotic. Would be great if you could you propose a workaround. Thanks!
…/dimorphite_dl-1.2.4/dimorphite_dl.py –smiles ‘CC(=O)N1CN(CN(C1)C(C)=O)C(C)=O’
For help, use: python dimorphite_dl.py –help
If you use Dimorphite-DL in your research, please cite:
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An
open-source program for enumerating the ionization states of drug-like small
molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.