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Int J Biol Sci 2018; 14(8):901-906. doi:10.7150/ijbs.24327

Research Paper

A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method

Han Wang1,2, Jingru Wang1,2, Li Zhang3, Pingping Sun1,2, Ning Du4, Yanwen Li1,2,✉

1. School of Information Science and Technology, Northeast Normal University, Changchun, 130117, China.
2. Institute of Computational Biology, Northeast Normal University, Changchun, 130117, China.
3. School of Computer Science and Engineering, Changchun University of Technology, Changchun, China.
4. School of Mathematics and Statistics, Northeast Normal University, Changchun, 130024, China


Alpha-helical transmembrane protein (αTMP) is one of the two major categories of transmembrane protein (TMP). They are abundant existing in eukaryotic cells and involved in many biological processes. The special physicochemical properties, the structures of αTMP are hard to be experimentally solved, but αTMP's sequential segments are important to determine their conformations, so that TM-specific alignment is necessary to benefit their structure prediction. We used segment information extracted from topology structure and evolutionary information as features to implement a αTMP Segment Alignment method (TMSA). The method was trained using one non-redundant dataset and tested using another non-redundant dataset. Comparing the results to a general alignment method HHalign, TMSA achieved higher alignment accuracy, and easier to recognize the fold of αTMPs.

Keywords: Transmembrane Protein, Segment Alignment, Topology

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license ( See for full terms and conditions.
How to cite this article:
Wang H, Wang J, Zhang L, Sun P, Du N, Li Y. A Sequential Segment Based Alpha-Helical Transmembrane Protein Alignment Method. Int J Biol Sci 2018; 14(8):901-906. doi:10.7150/ijbs.24327. Available from