No
Yes (multi-objective scoring)
Emergence and bifurcation modeling
No
Central
Hence, while AlphaFold2 can predict whether a single variant is structurally viable, our system actively explores the adaptive space, identifies function-enhancing mutations, and tracks population bifurcations in silico.
2. Rosetta and Structure-Based Design Engines
Rosetta is a gold-standard framework for de novo protein design and stability optimization, utilizing Monte Carlo sampling and energy minimization principles. It excels in:
Designing new folds or interfaces with high stability
Refining candidate structures based on backbone and side-chain energetics
However, Rosetta assumes a largely deterministic landscape of protein folding and does not model adaptive emergence or long-range network effects from system-level interactions---central in our CAS-based perspective.
