Chapter title |
Consensus Prediction of Charged Single Alpha-Helices with CSAHserver
|
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Chapter number | 3 |
Book title |
Prediction of Protein Secondary Structure
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6406-2_3 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6404-8, 978-1-4939-6406-2
|
Authors |
Dániel Dudola, Gábor Tóth, László Nyitray, Zoltán Gáspári |
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. |
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