A hybrid approach to protein folding problem integrating constraint programming with local search

Background: The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the computational hardness of this optimization problem. Heuristic search algorithms and constraint programming are two common techniques to approach this problem. The present study introduces a novel hybrid approach to simulate the protein folding problem using constraint programming technique integrated within local search. Results: Using the face-centered-cubic lattice model and 20 amino acid pairwise interactions energy function for the protein folding problem, a constraint programming technique has been applied to generate the neighbourhood conformations that are to be used in generic local search procedure. Experiments have been conducted for a few small and medium sized proteins. Results have been compared with both pure constraint programming approach and local search u...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel
• Keywords: BMCBI 2010, Constraint Programming, Local Search, Protein Folding Problem