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

Pandurangan Sundaramurthy,Ramanathan Sowdhamini,Khader Shameer,Sunita Gakkhar,Raashi Sreenivasan

doi:10.1186/1471-2105-11-s1-s24

Abstract

BackgroundFolding 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.ResultsWe 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.ConclusionHORI 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

Highlights

Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein
We describe the availability of a web server called HORI (Higher Order Residue Interactions in proteins) developed for the calculation of generic and specific higher order residue interaction patterns in protein structure
It has been proved that higher order residue interactions, up to the level of quadruple interactions, will play a major role in the three-dimensional structure of proteins

Summary

Introduction

Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein. Pairwise, triplet and quadruple based higher order residue interactions play a crucial role to attain the stable conformation of the protein structures. Higher order residue interactions contribute to the potential energy landscape of proteins and it is important to understand such interactions mediated in the level of active site residues to whole structure [1,2,3,4,5,6,7]. It has been proved that higher order residue interactions, up to the level of quadruple interactions, will play a major role in the three-dimensional structure of proteins. As HORI server can be used to compute higher order interactions in different levels from single residue to whole structure, analysis of higher order interactions mediated by residues in the functional or active sights will provide better insights to understand the structural interactions contributed by these important residues. We explain various feature of HORI server along with different example scenarios where the general application of the higher order interaction and the server is useful

Methods

Results

Conclusion