Exact Sequence Analysis for Three-Dimensional HP Lattice Proteins

Abstract

We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a non-degenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets.