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@keitaroyam keitaroyam commented Dec 6, 2025

In the monomer library, the link SS (not disulf) is defined for any peptide residues having the "SG" atom. This is dangerous, because accidental SS links can be made.

SS . CYS-SS peptide . CYS-SS peptide SS-bridge

In the current library, there are 77 peptide monomers having SG atom, but only 03Y CG6 CYS DCY LE1 LEI are SS-linkable (others have C-S-C bonds for example).

I checked the "disulfide" connections from mmcif headers of the pdb entries including these monomers (apart from CYS), and found the following patterns. The DCY-DCY link is already defined as "Ddisul".

('DCY', 'DCY') 40 pdb
('CYS', 'DCY') 5 pdb
('CYS', 'LE1') 3 pdb

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