Detection of single alpha-helices in large protein sequence sets using hardware acceleration

Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Single alpha-helices (SAHs) are increasingly recognized as important structural and functional elements of proteins. Comprehensive identification of SAH segments in large protein datasets was largely hindered by the slow speed of the most restrictive prediction tool for their identification, FT_CHARGE on common hardware. We have previously implemented an FPGA-based version of this tool allowing fast analysis of a large number of sequences. Using this implementation, we have set up of a semi-automated pipeline capable of analyzing full UniProt releases in reasonable time and compiling monthly updates of a comprehensive database of SAH segments. Releases of this database, denoted CSAHDB, is available on the CSAHserver 2 website at csahserver.itk.ppke.hu. An overview of human SAH-containing sequences combined with a literature survey suggests specific roles of SAH segments in proteins involved in RNA-based regulation processes as well as cytoskeletal proteins, a number of which is also linked to the development and function of synapses.

Original languageEnglish
Pages (from-to)109-116
Number of pages8
JournalJournal of Structural Biology
Volume204
Issue number1
DOIs
Publication statusPublished - Oct 2018

Keywords

  • Cytoskeleton
  • FPGA
  • Protein structure prediction
  • RNA processing
  • Single alpha-helix

ASJC Scopus subject areas

  • Structural Biology

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