Abstract
This paper presents a novel algorithm for drug design that unifies structural peptidomimetic engineering, molecular docking, substituent interactions, and configurational refinement. The algorithm consists of four key steps: Configuration Cloning (CC), Substituent Replacement and Strategic Functionalization Mechanism (SR-SFM), Manual Rotor Lock (MRL), and Structural Refinement via SMILES
Conversion. The Mathematical framework is developed to explain the efficacy of this approach in optimizing binding affinity, conformational stability, and interaction specificity.