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

Ákos Kovács, Dániel Dudola, L. Nyitray, Gábor Tóth, Zoltán Nagy, Z. 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
JournalJournal of Structural Biology
DOIs
Publication statusAccepted/In press - Jan 1 2018

Fingerprint

Proteins
Databases
Cytoskeletal Proteins
Synapses
alpha-Helical Protein Conformation
RNA
Surveys and Questionnaires
Datasets
Protein Structural Elements

Keywords

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

ASJC Scopus subject areas

  • Structural Biology

Cite this

Detection of single alpha-helices in large protein sequence sets using hardware acceleration. / Kovács, Ákos; Dudola, Dániel; Nyitray, L.; Tóth, Gábor; Nagy, Zoltán; Gáspári, Z.

In: Journal of Structural Biology, 01.01.2018.

Research output: Contribution to journalArticle

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AU - Gáspári, Z.

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