Neighborhood Selection in Constraint-Based Local Search for Protein Structure Prediction

Abstract

Protein structure prediction (PSP) is a very challenging constraint optimization problem. Constraint-based local search approaches have obtained promising results in solving constraint models for PSP. However, the neighborhood exploration policies adopted in these approaches either remain exhaustive or are based on random decisions. In this paper, we propose heuristics to intelligently explore only the promising areas of the search neighborhood. On face centered cubic lattice using a realistic 20ײ0 energy model and standard benchmark proteins, we obtain structures with significantly lower energy and RMSD values than those obtained by the state-of-the-art algorithms.