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A tool for the prediction of functionally important sites in proteins using a library of functional templates

Author(s): Christopher J. Lanczycki | Saikat Chakrabarti

Journal: Bioinformation
ISSN 0973-2063

Volume: 2;
Issue: 7;
Start page: 279;
Date: 2008;
Original page

Keywords: prediction | proteins | functional templates | library

Understanding and characterizing the biochemical and evolutionary information within the wealth of protein sequence and structural data, particularly at functionally important sites, is very important. A comprehensive analysis of physico-chemical properties and evolutionary conservation patterns at the molecular and biological function level is expected to yield important clues for identifying similar sites in as-yet uncharacterized proteins. We present a library of protein functional templates (PFTs) designed to represent the compositional and evolutionary conservation patterns of functional sites at the molecular and biological function level. Subsequently we developed LIMACS (LInear MAtching of Conservation Scores), a software tool that uses the template library for the prediction of functionally important sites in a multiple sequence alignment, transferring the molecular function annotation from the most-similar functional site in the template library to a predicted site.
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