Fig. 2
Overview of the genetic algorithm. Peptides obtained from the Propedia database were initially docked to the Mpro structure. The top 100 results were selected as the initial population for the genetic algorithm. Two strategies were then employed: a docking-based approach (utilizing the Rosetta suite) and an AI-driven 3D modeling approach (utilizing ColabFold). A fitness function evaluated peptide candidates through a tournament selection scheme, and genetic operations were applied to peptide sequences to generate a new population. Each new set of peptide structures was modeled through docking (Rosetta) or 3D modeling (ColabFold), resulting in a population of 25 structures. These steps were iterated over 100 generations. Finally, the best peptides from each generation were selected based on the lowest docking scores.
