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Title: Transmembrane helix : simple or complex
Authors: Wong, Wing-Cheong
Maurer-Stroh, Sebastian
Schneider, Georg
Eisenhaber, Frank
Keywords: DRNTU::Science::Biological sciences
Issue Date: 2012
Source: Wong, W.-C., Maurer-Stroh, S., Schneider, G., & Eisenhaber, F. (2012). Transmembrane helix: simple or complex. Nucleic Acids Research, 40(W1), W370-W375.
Series/Report no.: Nucleic acids research
Abstract: Transmembrane helical segments (TMs) can be classified into two groups of so-called ‘simple’ and ‘complex’ TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely accessible at or available for download.
DOI: 10.1093/nar/gks379
Rights: © 2012 The Authors. This paper was published in Nucleic Acids Research and is made available as an electronic reprint (preprint) with permission of The Authors. The paper can be found at the following official DOI: [].  One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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