  Protein structure prediction based on Hydrophobic-Polar energy model
essentially becomes searching for a conformation having a compact hydrophobic
core at the center. The hydrophobic core minimizes the interaction energy
between the amino acids of the given protein. Local search algorithms can
quickly find very good conformations by moving repeatedly from the current
solution to its "best" neighbor. However, once such a compact hydrophobic core
is found, the search stagnates and spends enormous effort in quest of an
alternative core. In this paper, we attempt to restructure segments of a
conformation with such compact core. We select one large segment or a number of
small segments and apply exhaustive local search. We also apply a mix of
heuristics so that one heuristic can help escape local minima of another. We
evaluated our algorithm by using Face Centered Cubic (FCC) Lattice on a set of
standard benchmark proteins and obtain significantly better results than that
of the state-of-the-art methods.
