title: On the difference in quality between current heuristic and optimal solutions to the protein structure alignment problem.
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.
authors.affiliation: Department of Computer Science, School of Engineering, Pontificia Universidad Católica de Chile, 4860 Avenue Vicuña Mackenna, 6904411 Santiago, Chile.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Arriagada
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Poleksic
mesh_terms: D000465:Algorithms; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software
chemical_list: D001426:Bacterial Proteins; D011506:Proteins