The SDRA server is dedicated to the analysis of the conserved core residues (CCR) and the specificity determining residues (SDR) in protein families.
CCR are usually important to either fold stability or functional interactions of all proteins in a protein family. SDR are often conserved in a specific protein sub-family and mostly absent outside this subfamily. SDR often determine the functional specificity of protein subfamilies.
The SDRA server aims to:
quickly assess the evolutive diversity of a protein family
statistically discriminate CCR and SDR
clearly highlight each phylogenetic subgroup sharing the same SDR signature
spatially analyze the atomic constraints which explain some CCR or SDR conservation
compare the 1D and 3D motifs conserved in different sub-families
The SDRA analysis process is based on the following steps:
After the user has provided a set of query proteins as data input, the server automatically looks for homologous sequences and structures, then clusters, filters, aligns and sorts them phylogenetically. The resulting multiple sequence alignment is then statistically analyzed to calculate conservation and specificity scores for each residue.
Each residue is then colorized using a coding scheme based on the HSL color space (Hue-Saturation-Lightness). The median phylogenetic index of the proteins with a given amino acid at a given alignment position is coded as the hue H. The specificity score of the residue is coded as the saturation S (SDR have saturated colors). The conservation score of the residue is coded as the lightness L (CCR are in black or dark gray).
The SDRA results are accessible from a web page where both the HSL-colorized sequence alignment and the corresponding structures are displayed. The structures can be spatially analyzed using the 3D viewer Jsmol and can be interactively colorized as the aligned sequences.
