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BioMed Research International
Volume 2013, Article ID 459248, 8 pages
Research Article

On the Difference in Quality between Current Heuristic and Optimal Solutions to the Protein Structure Alignment Problem

1Department of Computer Science, School of Engineering, Pontificia Universidad Católica de Chile, 4860 Avenue Vicuña Mackenna, 6904411 Santiago, Chile
2Department of Computer Science, University of Northern Iowa, 1227 West 27th Street, Cedar Falls, IA 50613, USA

Received 10 September 2012; Accepted 2 November 2012

Academic Editor: Tun-Wen Pai

Copyright © 2013 Mauricio Arriagada and Aleksandar Poleksic. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


The importance of pairwise protein structural comparison in biomedical research is fueling the search for algorithms capable of finding more accurate structural match of two input proteins in a timely manner. In recent years, we have witnessed rapid advances in the development of methods for approximate and optimal solutions to the protein structure matching problem. Albeit slow, these methods can be extremely useful in assessing the accuracy of more efficient, heuristic algorithms. We utilize a recently developed approximation algorithm for protein structure matching to demonstrate that a deep search of the protein superposition space leads to increased alignment accuracy with respect to many well-established measures of alignment quality. The results of our study suggest that a large and important part of the protein superposition space remains unexplored by current techniques for protein structure alignment.