Consensus Prediction of Charged Single Alpha-Helices with CSAHserver

Dudola, Dániel and Tóth, Gábor and Nyitray, László and Gáspári, Zoltán (2017) Consensus Prediction of Charged Single Alpha-Helices with CSAHserver. In: Prediction of Protein Secondary Structure. Methods in Molecular Biology,, 1484 . Springer, New York, pp. 25-34. ISBN 978-1-4939-6404-8

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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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