SPEER-SERVER: a web server for prediction of protein specificity determining sites

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or pro...

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Main Authors:	Chakraborty, Abhijit, Mandloi, Sapan, Lanczycki, Christopher J., Panchenko, Anna R., Chakrabarti, Saikat
Format:	Online
Language:	English
Published:	Oxford University Press 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394334/

id	pubmed-3394334
recordtype	oai_dc
spelling	pubmed-33943342012-07-30 SPEER-SERVER: a web server for prediction of protein specificity determining sites Chakraborty, Abhijit Mandloi, Sapan Lanczycki, Christopher J. Panchenko, Anna R. Chakrabarti, Saikat Articles Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. Oxford University Press 2012-07 2012-06-09 /pmc/articles/PMC3394334/ /pubmed/22689646 http://dx.doi.org/10.1093/nar/gks559 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Chakraborty, Abhijit Mandloi, Sapan Lanczycki, Christopher J. Panchenko, Anna R. Chakrabarti, Saikat
spellingShingle	Chakraborty, Abhijit Mandloi, Sapan Lanczycki, Christopher J. Panchenko, Anna R. Chakrabarti, Saikat SPEER-SERVER: a web server for prediction of protein specificity determining sites
author_facet	Chakraborty, Abhijit Mandloi, Sapan Lanczycki, Christopher J. Panchenko, Anna R. Chakrabarti, Saikat
author_sort	Chakraborty, Abhijit
title	SPEER-SERVER: a web server for prediction of protein specificity determining sites
title_short	SPEER-SERVER: a web server for prediction of protein specificity determining sites
title_full	SPEER-SERVER: a web server for prediction of protein specificity determining sites
title_fullStr	SPEER-SERVER: a web server for prediction of protein specificity determining sites
title_full_unstemmed	SPEER-SERVER: a web server for prediction of protein specificity determining sites
title_sort	speer-server: a web server for prediction of protein specificity determining sites
description	Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.
publisher	Oxford University Press
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394334/
_version_	1611542388557217792

SPEER-SERVER: a web server for prediction of protein specificity determining sites

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