title: Transmembrane helix: simple or complex.
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 http://tmsoc.bii.a-star.edu.sg or available for download.
authors.affiliation: Bioinformatics Institute (BII), Agency for Science, Technology and Research (A STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671. wongwc@bii.a-star.edu.sg
authors.forename: Wing-Cheong
authors.initials: WC
authors.lastname: Wong
authors.forename: Sebastian
authors.initials: S
authors.lastname: Maurer-Stroh
authors.forename: Georg
authors.initials: G
authors.lastname: Schneider
authors.forename: Frank
authors.initials: F
authors.lastname: Eisenhaber
mesh_terms: D000465:Algorithms; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D043886:Receptor, Cholecystokinin A / Q000737:chemistry; D012243:Rhodopsin / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D008565:Membrane Proteins; D043886:Receptor, Cholecystokinin A; D012243:Rhodopsin