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Cation-aromatic database
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DOI：10.1002/prot.21202.png)
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Abstract
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Cation-aromatic database (CAD) is a publicly available web-based database that aims to provide further understanding of interaction between a cation and the Tr-moiety of the aromatic residues in protein data bank (PDB). All the metal ions and basic amino acid residues are considered as cations. The motifs are defined on the basis of distance between the cation and the centroid of the aromatic ring. This generalized way of defining the motifs enables a thorough inspection and analysis of the type of interactions in proteins. Of these pairs, those having the cation within a cylinder with the arene ring as a base are identified. This geometric criterion enables the identification of strong cation-Tr interactions. A tool to identify the interactions in a user-given protein is also added to the database. CAD is freely accessible via the Internet at http://203.199.182.73/gnsmmg/ databases/cad/ Proteins 2007;67:1179-1184. (C) 2007 Wiley-Liss, Inc.
Keywords:
aromatic amino acids
cation-pi interactions
statistical analysis
metal interactions
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