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Faculty Publications
Algorithms For Optimal Protein Structure Alignment
Document Type
Article
Journal/Book/Conference Title
Bioinformatics
Volume
25
Issue
21
First Page
2751
Last Page
2756
Abstract
Motivation: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment problem, which has a polynomial time solution, the structural alignment problem has not been even classified as solvable. Results: We study one of the most widely used measures of protein structural similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. We prove that, for any two proteins, this measure can be optimized for all but finitely many distance cutoffs. Our method leads to a series of algorithms for optimizing other structure similarity measures, including the measures commonly used in protein structure prediction experiments. We also present a polynomial time algorithm for finding a near-optimal superposition of two proteins. Aside from having a relatively low cost, the algorithm for near-optimal solution returns a superposition of provable quality. In other words, the difference between the score of the returned superposition and the score of an optimal superposition can be explicitly computed and used to determine whether the returned superposition is, in fact, the best superposition. © The Author 2009. Published by Oxford University Press. All rights reserved.
Department
Department of Computer Science
Original Publication Date
11-9-2009
DOI of published version
10.1093/bioinformatics/btp530
Recommended Citation
Poleksic, Aleksandar, "Algorithms For Optimal Protein Structure Alignment" (2009). Faculty Publications. 2201.
https://scholarworks.uni.edu/facpub/2201