In our CAS-guided framework, a protein is abstracted as a residue-residue interaction graph G=(V,E)G = (V, E), where:
V={r1,r2,...,rn}V = \{r_1, r_2, \ldots, r_n\} denotes residues (amino acids),
E={(ri,rj)dij<}E = \{(r_i, r_j) | d_{ij} < \delta\} encodes interactions based on spatial distance, energy thresholds, or co-evolutionary signals.
Edges are weighted by a function wijw_{ij}, which can incorporate:
Van der Waals or electrostatic potential,
Hydrogen bonding frequency,
Contact probability from molecular dynamics (MD) simulations,
Or even evolutionary coupling scores from multiple sequence alignments.
This transforms the static polypeptide chain into a living, interacting system, amenable to graph-theoretic measures such as:
Degree centrality (residue importance),
Betweenness (pathway bottlenecks),
