Modularity (subdomain segmentation),
Spectral clustering (emergent folding units).
2. Integration with CAS Variables
Each graph property corresponds to a CAS parameter, allowing multidimensional tracking of systemic evolution:
This systemic mapping allows for real-time simulation of evolutionary dynamics, where the protein graph adapts in response to mutations, environmental changes, or selection pressures.
3. Mutation as Graph Perturbation
In our model, mutations are conceptualized as localized perturbations to the graph:
A point mutation at residue rkr_k modifies the local node weight and its adjacent edge weights wkjw_{kj},
Insertions/deletions alter the graph topology by adding/removing nodes and edges,
Structural mutations may induce long-range rewiring, impacting modular integrity or allosteric communication paths.
