Link: https://consurf.tau.ac.il/
Overview: https://consurf.tau.ac.il/overview.php
The ConSurf server (Glaser et al., 2003; Landau et al., 2005; Ashkenazy et al., 2010; Celniker et al., 2013; Ashkenazy et al., 2016) is a bioinformatics tool for estimating the evolutionary conservation of amino/nucleic acid positions in a protein/DNA/RNA molecule based on the phylogenetic relations between homologous sequences. The degree to which an amino (or nucleic) acid position is evolutionarily conserved (i.e., its evolutionary rate) is strongly dependent on its structural and functional importance. Thus, conservation analysis of positions among members from the same family can often reveal the importance of each position for the protein (or nucleic acid)’s structure or function. In ConSurf, the evolutionary rate is estimated based on the evolutionary relatedness between the protein (DNA/RNA) and its homologs and considering the similarity between amino (nucleic) acids as reflected in the substitutions matrix (Pupko et al., 2002; Mayrose et al., 2004).
Type in the PDB identifier of the structure you are interested in
What the ConSurf Server will do:
- Extract the sequence from the PDB file
- Find sequence homologs
- Create a multiple sequence alignment of the sequences
- Select the best evolutionary model
- Calculate conservation scores
- Project conservation scores onto the model.
The results page will provide additional information about the alignment and homologous sequences selected. You can view the color-coded model on a ConSurf page or in FirstGlance in Jmol. The color scale indicates the level of amino acid conservation. You can view the multiple sequence alignment and a phylogenetic tree using the browser-based application WASABI. Another ConSurf page will display the MSA color-coded by conservation, or this information is available in a chart format, as well.