CSAH server
 
Detect Charged Single α-Helices in protein sequences
Description Example CSAH Server Download
 

Description of the server

Charged single α-helices and their identification are described in:
  • Dániel Süveges, Zoltán Gáspári, Gábor Tóth, László Nyitray:
    Charged single α-helix: a versatile protein structural motif
    Proteins (2009) 74:905-916.
    [abstract]
Descriptions of the most recent version of CSAH server is published in:
  • Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári:
    Detection of single alpha-helices in large protein sequence sets using hardware acceleration
    J. Struct. Biol. (2018) 204:109-116.
    [abstract]

    This paper describes the adjustments of the default FT_CHARGE parameters to enhance sensitivity of the method along with a modified version of the helicity filter.

  • Dániel Dudola, Gábor Tóth, László Nyitray, Zoltán Gáspári:
    Consensus prediction of charged single alpha-helices with CSAHserver
    Zhou, Kloczkowski, Faraggi, Yang (eds): Prediction of Protein Secondary Structure
    Methods Mol Biol Vol. 1484, Springer, 2017, pp. 25-34.
    [abstract]

    This chapter describes practical usage of the method along with the introduction of a filtering step to discard hits with negligible α-helix forming propensity.

The original version of the server was published in:



The CSAH server offers two independent methods for CSAH detection in protein sequences: SCAN4CSAH and FT_CHARGE. SCAN4CSAH is based on a scoring scheme favoring ionic interactions important in the stabilization of CSAHs, whereas FT_CHARGE identifies repeated charge patterns using Fourier transformation. Both methods report P-values denoting the probability of the observed score arising by chance. Detailed description of the calculations is available in the papers above.

By default, the server invokes both methods on the submitted (single) sequence and reports their consensus. The minimum length of the consensus CSAHs is the lower of the following two values: i) the minimum CSAH length in SCAN4CSAH (default: 30) and ii) the window length in FT_CHARGE (default: 32-64 meaning that both 32 and 64-residue long segments will be scanned). For both methods, only CSAH segments wth P-values lower than 0.01 are reported by the server. The resulting CSAH sequence is checked for helicity based on Chou-Fasman helical propensity (Pα) parameters in order to omit hits that are unlikely to form α-helical structures in solution (e.g. seqments with multiple proline residues). The web interface allows the use of only one of the programs and allows limited parametrization (minimum CSAH length for SCAN4CSAH, window length(s) for FT_CHARGE).

Downloadable versions of both SCAN4CSAH and FT_CHARGE are provided along with a wrapper script to produce consensus and uniformly formatted output. The programs were written in Perl and allow full parametrization of the methods. The programs, along with an installer script and sample input/output files can be found on the Downloads page.

CSAHserver is maintained by Zoltán Gáspári (<gaspari.zoltan> at <itk.ppke.hu>).
 
Questions and suggestions regarding the CSAH server should go to Zoltán Gáspári (gaspari.zoltan at itk.ppke.hu)
© ZG & GT, 2009, 2015