CAPS-DB: A structural classification of helix-capping motifs

Segura, Joan; Oliva Miguel, Baldomero; Fernández Fuentes, Narcís

doi:http://dx.doi.org/10.1093/nar/gkr879

CAPS-DB: A structural classification of helix-capping motifs

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Segura J, Oliva B, Fernandez-Fuentes N. CAPS-DB: A structural classification of helix-capping motifs. Nucleic Acids Research. 2012;40(D1):D479-D485. DO:I 10.1093/nar/gkr879

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.