Comparison of Benchmark HP Model Proteins on Face-Centered Cubic and Simple Cubic Lattices using Replica-Exchange Wang-Landau Sampling

Abstract

Abstract The HP model represents protein sequences by coarse-graining amino acid types as either hydrophobic (H) or polar (P). This model has been studied extensively, where the simple cubic (sc) lattice is a commonly used for simplicity and efficiency, despite a limited ability to geometrically represent protein structures. One straightforward improvement is to instead use the face-centered cubic (fcc) lattice, which offers a more realistic geometry while retaining simplicity. Using the replica-exchange Wang-Landau algorithm, the ground state energies and full density of states are predicted for a set of biologically-motivated HP sequences on the fcc lattice. A direct thermodynamic comparison is made between the folding on fcc and sc lattices, and structural properties are calculated to further examine the folding on the fcc lattice.