"On Complexity Of Protein Structure Alignment Problem Under Distance Co" by Aleksandar Poleksic
 

Faculty Publications

On Complexity Of Protein Structure Alignment Problem Under Distance Constraint

Document Type

Article

Keywords

alignment algorithms, Protein structure, structural alignment, structural similarity

Journal/Book/Conference Title

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volume

9

Issue

2

First Page

511

Last Page

516

Abstract

We study the well-known Largest Common Point-set (LCP) under Bottleneck Distance Problem. Given two proteins a and b (as sequences of points in three-dimensional space) and a distance cutoff σ, the goal is to find a spatial superposition and an alignment that maximizes the number of pairs of points from a and b that can be fit under the distance σ from each other. The best to date algorithms for approximate and exact solution to this problem run in time O(n 8 ) and O(n 32), respectively, where n represents protein length. This work improves runtime of the approximation algorithm and the expected runtime of the algorithm for absolute optimum for both order-dependent and order-independent alignments. More specifically, our algorithms for near-optimal and optimal sequential alignments run in time O(n 7log n) and O(n 14log n), respectively. For nonsequential alignments, corresponding running times are O(n 7.5) and O(n 14.5). © 2012 IEEE.

Department

Department of Computer Science

Original Publication Date

2-6-2012

DOI of published version

10.1109/TCBB.2011.133

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