CAPS-DB: A Structural Classification of Helix-Capping Motifs

Nucleic Acids Res. 2012 Jan;40(Database issue):D479-85. doi: 10.1093/nar/gkr879. Epub 2011 Oct 22.

Abstract

The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (Φ-ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. The database is accessible at: http://www.bioinsilico.org/CAPSDB.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Motifs*
  • Cluster Analysis
  • Databases, Protein*
  • Models, Molecular
  • Peptides / chemistry
  • Protein Structure, Secondary
  • User-Computer Interface

Substances

  • Peptides