'SPEER-SERVER' is a web server that encodes the specific conservation pattern of amino acid types in a protein family to identify the specificity determining sites (SDS). The specific conservation pattern is predicted using amino acids' physico-chemical properties, relative entropy and the evolutionary rates between the protein subfamilies.
This is the first web server version of the original stand alone 'SPEER' program reported in the following article.
"Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids", Chakrabarti S, Bryant SH, Panchenko AR (2007). J Mol Biol. 373(3):801-10.PubMed ID: 17868687.
Features of SPEER-SERVER:
1. Representation of SPEER scores (specificity scores) onto the alignment. Visual representation of subfamilies/subgroups onto the alignment.
2. Projection of SPEER-SERVER predicted sites onto the representative three dimensional (3D) structures.
3. Representation of Cα-Cα structural distances between the SPEER-SERVER predicted SDS in the form of matrix and dendrogram.
4. Coevolutionary connections of SPEER-SERVER predicted SDS.
5. Option for identification of SDS using protein sequences instead of multiple sequence alignment.
6. Option for identification of SDS using automated subgrouping method i.e SCI-PHY OR SECATOR in case of protein families without subfamilies/subgroups information.
7. Identification of SDS in batch mode for large scale analysis.
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