Inhibitor peptide design for NF-кB: Markov model & genetic algorithm

Two peptide design approaches are proposed to block activities of disease related proteins. First approach employs a probabilistic method; the problem is set as Markov chain. The possible binding site of target protein and a path on this binding site are determined. 20 natural amino acids and 400 dipeptides are docked to the selected path using the AutoDock software. The statistical weight matrices for the binding energies are derived from AutoDock results; matrices are used to determine top 100 peptide sequences with affinity to target protein. Second approach utilizes a heuristic method for peptide sequence determination; genetic algorithm (GA) with tournament selection. The amino acids are the genes; the peptide sequences are the chromosomes of GA. Initial random population of 100 chromosomes leads to determination of 100 possible binding peptides, after 8-10 generations of GA. Thermodynamic properties of the peptides are analyzed by a method that we proposed previously. NF-κB protein is selected as case-study.