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Consensus Prediction of Charged Single Alpha-Helices with CSAHserver

  • Dániel Dudola
  • Gábor Tóth
  • László Nyitray
  • Zoltán GáspáriEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1484)

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.

Key words

Charged single alpha-helix Charged residues Consensus prediction Ion pairs Fourier transform Helicity Coiled coil 

Notes

Acknowledgments

This work was supported by a grant from the Hungarian Scientific Research Fund (OTKA/NKFIH NF104198). Z.G. was also supported by a János Bolyai Research Fellowship from the Hungarian Academy of Sciences.

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Dániel Dudola
    • 1
  • Gábor Tóth
    • 2
  • László Nyitray
    • 3
  • Zoltán Gáspári
    • 1
    Email author
  1. 1.Faculty of Information Technology and BionicsPázmány Péter Catholic UniversityBudapestHungary
  2. 2.Department of Medical and Biological SciencesNational Research, Development and Innovation OfficeBudapestHungary
  3. 3.Department of BiochemistryEötvös Loránd UniversityBudapestHungary

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