Beyond Bioinformatics

Title

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

Authors

Christopher J. Lanczycki¹ and Saikat Chakrabarti^1, *

Affiliation

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

Email

chakraba@ncbi.nlm.nih.gov; * Corresponding author

Article Type

Software

Date

received February 05, 2008; accepted February 11, 2008; published February 22, 2008

Abstract

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.

The PFT library, the LIMACS program and source code are available for PC, Mac and Linux operating systems from ftp://ftp.ncbi.nih.gov/pub/lanczyck/limacs.

Keywords

prediction; proteins; functional templates; library

Citation

Lanczycki and Chakrabarti, Bioinformation 2(7): 279-283 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.