A Hybrid Local Search for Simplified Protein Structure Prediction

2013 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms   unpublished
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 just by repeatedly moving from the current one to one of its "best" neighbor. However, once such a compact hydrophobic core is found, the search stagnates and spends
more » ... ormous effort in quest of an alternative core. In this paper, we attempt to restructure segments of a conformation that has a very compact core. The segments are conformation segments where an exhaustive search is locally applied. We also apply a mix of heuristics so that one of them could help while another takes into stagnation. We evaluate 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.
doi:10.5220/0004239401580163 fatcat:crkdrgj2m5el7afxmzvbrott5y