A new off-lattice HP model with side-chains for protein folding problem

Abstract

A HP like nonlinear programming model and a “brutforce” algorithm is proposed. The model takes into account highest degree of complexity – different size of radiuses of side-chains, mentioned below as radicals, and two stages of the algorithm, including random structure initially and subsequent purposeful folding process according to the physical forces and energies. The very preliminary computational runs favourably demonstrate the adequateness of the model and the efficiency of the algorithm.