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

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....

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Autores principales: Sundaramurthy, Pandurangan, Shameer, Khader, Sreenivasan, Raashi, Gakkhar, Sunita, Sowdhamini, Ramanathan
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009495/
https://www.ncbi.nlm.nih.gov/pubmed/20122196
http://dx.doi.org/10.1186/1471-2105-11-S1-S24
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author Sundaramurthy, Pandurangan
Shameer, Khader
Sreenivasan, Raashi
Gakkhar, Sunita
Sowdhamini, Ramanathan
author_facet Sundaramurthy, Pandurangan
Shameer, Khader
Sreenivasan, Raashi
Gakkhar, Sunita
Sowdhamini, Ramanathan
author_sort Sundaramurthy, Pandurangan
collection PubMed
description 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
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spelling pubmed-30094952010-12-23 HORI: a web server to compute Higher Order Residue Interactions in protein structures Sundaramurthy, Pandurangan Shameer, Khader Sreenivasan, Raashi Gakkhar, Sunita Sowdhamini, Ramanathan BMC Bioinformatics Research 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 BioMed Central 2010-01-18 /pmc/articles/PMC3009495/ /pubmed/20122196 http://dx.doi.org/10.1186/1471-2105-11-S1-S24 Text en Copyright ©2010 Sundaramurthy et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Sundaramurthy, Pandurangan
Shameer, Khader
Sreenivasan, Raashi
Gakkhar, Sunita
Sowdhamini, Ramanathan
HORI: a web server to compute Higher Order Residue Interactions in protein structures
title HORI: a web server to compute Higher Order Residue Interactions in protein structures
title_full HORI: a web server to compute Higher Order Residue Interactions in protein structures
title_fullStr HORI: a web server to compute Higher Order Residue Interactions in protein structures
title_full_unstemmed HORI: a web server to compute Higher Order Residue Interactions in protein structures
title_short HORI: a web server to compute Higher Order Residue Interactions in protein structures
title_sort hori: a web server to compute higher order residue interactions in protein structures
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009495/
https://www.ncbi.nlm.nih.gov/pubmed/20122196
http://dx.doi.org/10.1186/1471-2105-11-S1-S24
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