A simple and fast heuristic for protein structure comparison

Background: Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers. Results: We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1) from an optimization point of view the strategy is tested on

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: David A. Pelta, Juan Ramón González, Marcos Moreno Vega
• Keywords: BMCBI 2008, Map Overlap Problem, Protein Structure Comparison, Variable Neighborhood Search