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SSEP: Secondary structural elements of proteins.

V Shanthi1, P Selvarani, Ch Kiran Kumar

  • 1Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

Nucleic Acids Research
|June 26, 2003
PubMed
Summary

The Secondary Structure Element database (SSEP) offers extensive information on protein secondary structures, including alpha-helices and beta-strands. This resource aids researchers in exploring protein structural elements and their 3D visualizations.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein secondary structures are crucial for protein function and stability.
  • Comprehensive databases are needed to access and analyze these structural elements.

Purpose of the Study:

  • To present the Secondary Structure Element database (SSEP), a resource for secondary structural elements in protein chains.
  • To provide detailed information on various secondary structural elements and enable 3D visualization.

Main Methods:

  • Curated data from 25% and 90% non-redundant protein chain sets.
  • Inclusion of alpha-helical segments, beta-strand fragments, 3(10)-helix, beta- and nu-turns, and hairpin loops.
  • Integration with the RASMOL program for 3D structure visualization.

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Main Results:

  • SSEP contains data for 1771 protein chains (25% non-redundant) and 6182 protein chains (90% non-redundant).
  • The database details secondary structural elements of varying lengths.
  • Users can visualize queried secondary structural fragments in 3D using RASMOL.

Conclusions:

  • SSEP serves as a valuable, regularly updated resource for protein secondary structure analysis.
  • The database facilitates research in structural biology and bioinformatics through accessible data and visualization tools.