Faculty Publications

Title

Optimal pairwise alignment of fixed protein structures in subquadratic time

Document Type

Article

Keywords

alignment, dynamic programming, Protein structure, structure comparison

Journal/Book/Conference Title

Journal of Bioinformatics and Computational Biology

Volume

9

Issue

3

First Page

367

Last Page

382

Abstract

The problem of finding an optimal structural alignment for a pair of superimposed proteins is often amenable to the SmithWaterman dynamic programming algorithm, which runs in time proportional to the product of lengths of the sequences being aligned. While the quadratic running time is acceptable for computing a single alignment of two fixed protein structures, the time complexity becomes a bottleneck when running the SmithWaterman routine multiple times in order to find a globally optimal superposition and alignment of the input proteins. We present a subquadratic running time algorithm capable of computing an alignment that optimizes one of the most widely used measures of protein structure similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. The algorithm presented in this article can be used to significantly improve the speedaccuracy tradeoff in a number of popular protein structure alignment methods. © 2011 Imperial College Press.

Original Publication Date

6-1-2011

DOI of published version

10.1142/S0219720011005562

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