In this project, the work done by Ken Dill on the subject is reproduced. In particular, proteins are modeled as a heteropolymer of hydrophobic (H) or polar (P) residues. All possible arrangements of these monomers are enumerated exhaustively on a simple cubic lattice (ignoring connectivity) to obtain the arrangement(s) of minimal surface area. This was the focus of our research. In his original paper, Dill proceeds to find all native states by applying a threading algorithm to these structures. This so-called Constrained Hydrophobic Core Construction (CHCC) method is considerably more efficient than previous methods, and allows proteins of realistic length (up to 80-mers) to be folded on a lattice. |
