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Volume 11   Issue 2   Year 2016
Application of Taguchi Method for Optimization of the Peptide Ligand Structure

Danilkovich A.V., Turobov V.I., Sobolev E.V., Udovichenko I.P.

Branch of the M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
Pushchino State Institute of Natural Sciences, Pushchino, Russia
Institute of Mathematical Problems of Biology – Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
EMBL Hamburg, Hamburg, Germany

Abstract. 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.

 

Key words: Taguchi method, structure optimization, molecular modeling, primary structure.

 
Table of Contents Original Article
Math. Biol. Bioinf.
2016;11(2):385-393
doi: 10.17537/2016.11.385
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References

 

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