A New Algorithm for 2D Hydrophobic-Polar Model: An Algorithm Based on Hydrophobic Core in Square Lattice

This study was engage in a new algorithm which was used to solve the problem of protein folding. The conformation of hydrophobic core of protein was key factor of structure of protein. So, in our algorithm, we set a hydrophobic core which was restricted by new aggregate. Then, the hydrophilic residues between two hydrophobic residues were ranged, the optimal conformation was gained if all residues were not overlap and continuous. The algorithm in this study can be prevented effecttively falls into partially smallest energy.