Paper Info
Title
SPEER-SERVER: a web server for prediction of protein specificity determining sites.
Abstract
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/.
Year
DOI
Venue
2012
10.1093/nar/gks559
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
amino acids,protein binding,proteins,algorithms,sequence alignment,internet
Sequence alignment,Protein family,Data visualization,Biology,Input/output,Bioinformatics,Computational biology,Genetics,Web server,The Internet
Journal
Volume
Issue
ISSN
40
W1
0305-1048
Citations 
PageRank 
References 
3
0.49
21
Authors
5
Name
Order
Citations
PageRank
Abhijit Chakraborty1101.37
Sapan Mandloi230.49
Christopher J Lanczycki3426172.22
Anna R. Panchenko4907252.52
Saikat Chakrabarti518821.86