Faculty Publications

Title

On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem

Document Type

Article

Journal/Book/Conference Title

BioMed Research International

Volume

2013

Abstract

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. © 2013 Mauricio Arriagada and Aleksandar Poleksic.

Original Publication Date

3-11-2013

DOI of published version

10.1155/2013/459248

Share

COinS