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This article is part of the supplement: Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

Open Access Research

HORI: a web server to compute Higher Order Residue Interactions in protein structures

Pandurangan Sundaramurthy124, Khader Shameer1, Raashi Sreenivasan135, Sunita Gakkhar2 and Ramanathan Sowdhamini1*

  • * Corresponding author: Ramanathan Sowdhamini mini@ncbs.res.in

  • † Equal contributors

Author Affiliations

1 National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, 560065, India

2 Department of Mathematics, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India

3 Centre for Biotechnology, Anna University, Chennai 600025, India

4 Department of Bioinformatics, School of Biotechnology, Karunya University, Coimbatore - 641114, India

5 University of Wisconsin-Madison, Madison, WI 53706-1481, USA

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BMC Bioinformatics 2010, 11(Suppl 1):S24  doi:10.1186/1471-2105-11-S1-S24

Published: 18 January 2010

Abstract

Background

Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein. Higher order residue interactions, like pairwise, triplet and quadruplet ones, play a vital role in attaining the stable conformation of the protein structure. It is generally agreed that higher order interactions make significant contribution to the potential energy landscape of folded proteins and therefore it is important to identify them to estimate their contributions to overall stability of a protein structure.

Results

We developed HORI [Higher order residue interactions in proteins], a web server for the calculation of global and local higher order interactions in protein structures. The basic algorithm of HORI is designed based on the classical concept of four-body nearest-neighbour propensities of amino-acid residues. It has been proved that higher order residue interactions up to the level of quadruple interactions plays a major role in the three-dimensional structure of proteins and is an important feature that can be used in protein structure analysis.

Conclusion

HORI server will be a useful resource for the structural bioinformatics community to perform analysis on protein structures based on higher order residue interactions. HORI server is a highly interactive web server designed in three modules that enables the user to analyse higher order residue interactions in protein structures. HORI server is available from the URL: http://caps.ncbs.res.in/hori webcite