Protein folding of the HOP model: A parallel Wang - Landau study

Abstract

We propose a simple modification to the hydrophobic-polar (HP) protein model, by introducing a new type of monomer, "0", with intermediate hydrophobicity of some amino acids between H and P. With the replica-exchange Wang-Landau sampling method, we investigate some widely studied HP sequences as well as their H0P counterparts and observe that the H0P sequences exhibit dramatically reduced ground state degeneracy and more significant transition signals at low temperature for some thermodynamic properties, such as the specific heat.