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Mathematical Problems in Engineering
Volume 2013, Article ID 541359, 10 pages
Research Article

A Topology Structure Based Outer Membrane Proteins Segment Alignment Method

1School of Computer Science and Information Technology, Northeast Normal University, Changchun 130024, China
2Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China
3School of Physical Education, Northeast Normal University, Changchun 130117, China
4National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun 130024, China

Received 15 July 2013; Accepted 7 September 2013

Academic Editor: William Guo

Copyright © 2013 Han Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Outer membrane proteins (OMPs) are transmembrane proteins (TMPs) located in outer membranes. These proteins perform diverse biochemical functions and have immediate medical relevance, so that their spatial structures are important for studying. But the special physicochemical properties of OMP make it hard to obtain their structures experimentally. For the purpose of predicting OMP structures, discriminating OMPs and aligning their sequences to native structures are indispensable steps. We developed a novel method OMSA (Outer Membrane Segment Alignment), which implemented both steps in one program. OMSA integrates OMP-specific topology features to implement a sequence-to-structure alignment, for example, segment type and segment orientation, while a segment-dependent gap penalty model is employed to improve the alignment. Compared to peer top-leading methods, OMSA achieved higher accuracy in both OMP discrimination and alignment, which may further improve OMP structure studying.