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Open Access Highly Accessed Methodology article

A simple and fast heuristic for protein structure comparison

David A Pelta1*, Juan R González1* and Marcos Moreno Vega2

Author Affiliations

1 Models of Decision and Optimization Research Group, Dept. of Computer Science and Artificial Intelligence, University of Granada, Spain

2 Department of Statistics, Operations Research and Computation (DEIOC), University of La Laguna, Spain

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BMC Bioinformatics 2008, 9:161  doi:10.1186/1471-2105-9-161

Published: 25 March 2008



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.


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 two different datasets, obtaining an error of 3.5%(over 2702 pairs) and 1.7% (over 161 pairs) with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2) in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level.


We designed, implemented and tested.a new tool for solving MAX-CMO, based on a well-known metaheuristic technique. The good balance between solution's quality and computational effort makes it a valuable tool. Moreover, to the best of our knowledge, this is the first time the MAX-CMO measure is tested at SCOP's fold and CATH's architecture levels with encouraging results.

Software is available for download at webcite.