Application of taguchi method for optimization of the peptide ligand structure

Taguchi method was used to optimize peptide ligand structure using the H-2/TCR complex (PDB ID 2Z31). This approach greatly reduces the number of experiments that are required to analyze the contribution of various amino acid residues for each position into ligand molecule. Taguchi matrix was used to design a set of peptide ligands for molecular docking and molecular mechanics energy minimization. This approach allowed creating a new peptide structure with lower molecular mechanics energy than native peptide and demonstrates the applicability of the Taguchi method for peptide ligand optimization.