title: Consensus Prediction of Charged Single Alpha-Helices with CSAHserver.
abstract: Charged single alpha-helices (CSAHs) constitute a rare structural motif. CSAH is characterized by a high density of regularly alternating residues with positively and negatively charged side chains. Such segments exhibit unique structural properties; however, there are only a handful of proteins where its existence is experimentally verified. Therefore, establishing a pipeline that is capable of predicting the presence of CSAH segments with a low false positive rate is of considerable importance. Here we describe a consensus-based approach that relies on two conceptually different CSAH detection methods and a final filter based on the estimated helix-forming capabilities of the segments. This pipeline was shown to be capable of identifying previously uncharacterized CSAH segments that could be verified experimentally. The method is available as a web server at http://csahserver.itk.ppke.hu and also a downloadable standalone program suitable to scan larger sequence collections.
authors: Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest, 1083, Hungary.
authors: Dániel
authors: D
authors: Dudola
authors: Department of Medical and Biological Sciences, National Research, Development and Innovation Office, Budapest, Hungary.
authors: Gábor
authors: G
authors: Tóth
authors: Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.
authors: László
authors: L
authors: Nyitray
authors: Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest, 1083, Hungary. gaspari.zoltan@gmail.com.
authors: Zoltán
authors: Z
authors: Gáspári
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D008958:Models, Molecular; D000072756:Protein Conformation, alpha-Helical; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D012984:Software
chemical_list: D011506:Proteins
keywords: Charged residues; Charged single alpha-helix; Coiled coil; Consensus prediction; Fourier transform; Helicity; Ion pairs