Put the crosslink into the representation
The method examines sulfur geometry and assignment confidence, then encodes selected covalent bonds alongside the chain’s topology. It distinguishes confident bond assignments, apparently free cysteines and unresolved cases. Those categories matter before a site is passed to covalent-design methods.
A chemical constraint that travels into the next calculation
Protein-topology resources already address crosslinks: KnotProt includes structures defined using disulfide or ion bonds. BioTwin’s intended contribution is to carry bond availability and uncertainty through its own conformer, access and covalent-engagement analyses. A geometric opening at a bonded cysteine should lead to a different chemistry question from an opening at a free thiol.
Use the assignment, inspect its confidence
A narrow computational calibration distinguished plausible crosslink patterns from uncertain structural assignments. Redox conditions and source-structure quality still need review. Selected invariants do not establish complete topological identity, and local coordinate stability does not prove a global chemical assignment. The method is useful when preserving these constraints changes which sites merit follow-up.