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

Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal 700032, India.
Nucleic Acids Research (Impact Factor: 9.11). 06/2012; 40(Web Server issue):W242-8. DOI: 10.1093/nar/gks559
Source: PubMed


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

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    • "A combined approach was also used to predict protein-protein interactions in complexes (e.g., Lasker et al., 2012, 2010), and to study signal transduction pathways (e.g., Aloy and Russell, 2002; Hosur et al., 2012) and interactions on a genome scale (e.g., Zhang et al., 2012). It was also used to study specificity-determining (e.g., Chakraborty et al., 2012) and co-evolving (e.g., de Juan et al., 2013; Marks et al., 2012) amino acids. Finally, scholars used the aforementioned existing tools to study specific protein families (e.g., Seffernick et al., 2009; Sukovich et al., 2010) and proteins (e.g., Raucci et al., 2014; Singh et al., 2014). "
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