It is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.
The regions of the polypeptide chain immediately preceding or following an ��������-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing ��������-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 (��������-����?)-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.
* PDB structures: 4591
* Number of clusters: 859
* Number of caps: 31452
Resource Type: Resource
Version: Latest Version
structural classification, helix-capping, protein engineering, clustering
Research Councils United Kingdom, Leeds Institute of Molecular Medicine, MICINN, FEDER, BIO2011-22568
Additional Resource Types
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Resource PubMed IDs
PMID: 22021380, PMID: 22144685
Created 3 years ago by Anonymous