Fig. 1

BpForms’ and BcForms’ representation of the primary structures of polymers and complexes. For example, BcForms represents a disulfide-linked dimer of the selenocysteine-modified tripeptide ACU (a, green box) as a set of polymeric subunits and crosslinks (c, green text), BpForms represents each tripeptide (b, blue boxes) as a sequence of residues (d, blue text), the protein alphabet represents the molecular structure of each residue and the atoms in each residue which are involved in bonds with adjacent residues (e, white boxes, green lines, and orange and blue letters), and the ontology of crosslinks represents the atoms involved in each crosslink (f, red line and red letters). BpForms uses SMILES to represent the molecular structure of each residue. The blue, black, and gray numbers illustrate the coordinate of each subunit, residue, and atom, respectively