2. Modular Structure of the Engine
The proposed architecture consists of four core modules, each representing a CAS layer that interacts with the others in adaptive feedback loops:
a. Genotype Generator Module
Generates or imports sequence variants (mutants) using evolutionary operations: Point mutations. Domain recombination. Insertions/deletions.Â
Evolutionary constraints can be encoded via probabilistic mutation matrices or codon-bias weighted graphs.
Integrates thermodynamic thresholds to discard immediately unviable candidates.
b. Folding & Structural Topology Module
Utilizes coarse-grained simulations (e.g., fragment assembly, graph neural nets) to predict fold topologies and contact maps.
Maps sequences to adaptive residue-interaction graphs, enabling downstream systems to track fold stability and topology changes.
c. Functional Evaluation Module
Applies binding energy estimation (via docking or energy functions) and catalytic efficiency prediction (e.g., using regression models trained on experimental data).
