dc.contributor.authorWong, Wing-Cheong
dc.contributor.authorMaurer-Stroh, Sebastian
dc.contributor.authorSchneider, Georg
dc.contributor.authorEisenhaber, Frank
dc.identifier.citationWong, W.-C., Maurer-Stroh, S., Schneider, G., & Eisenhaber, F. (2012). Transmembrane helix: simple or complex. Nucleic Acids Research, 40(W1), W370-W375.en_US
dc.description.abstractTransmembrane 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 http://tmsoc.bii.a-star.edu.sg or available for download.en_US
dc.relation.ispartofseriesNucleic acids researchen_US
dc.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: [http://dx.doi.org/10.1093/nar/gks379].  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.en_US
dc.subjectDRNTU::Science::Biological sciences
dc.titleTransmembrane helix : simple or complexen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Biological Sciencesen_US
dc.contributor.schoolSchool of Computer Engineering
dc.description.versionPublished versionen_US

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