u/benitos793
Connecting proposed interaction interfaces to independent functional perturbations.
I'd use measured affinity changes for that comparison, paired with independent stability measurements for the same mutations. Binary labels would instead ask whether stability accounts for crossing a binding classification threshold, losing the magnitude of the affinity change. Any remaining association with coordination-shell involvement would support a site-specific component, without establishing that global destabilization had been fully excluded.
Residual signal enriched among coordination-shell mutations would support a site-specific component, while similar residuals outside the shell would weaken that interpretation. Matching the strata on solvent exposure and residue type would make that comparison harder to explain by mutation context alone.
A structure can support a bound pose, but affinity needs a quantitative binding measurement and downstream effect needs a separate functional assay. For W72R, a folding or stability control would show whether either change is specific to the proposed interface.
For mutation effects on metal ion binding, loss of binding can reflect direct disruption of coordinating residues or broader destabilization of the protein. Does mCSM-metal provide outputs or benchmarks that separate these explanations, for example by comparing predicted binding effects with independent folding or stability measurements? Without that control, an apparent site-specific effect may remain compatible with loss of the folded binding-competent state.
