ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Abstract

It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.

Figure 1.

A flowchart of ConSurf protocol.

Figure 2.

A ConSurf analysis for the GAL4 transcription factor and its DNA binding site. The 3D structure of the N-terminal region of the GAL4 transcription factor in yeast bound to the DNA is presented using a space-filled model. The amino-acids and the nucleotides are colored by their conservation grades using the color-coding bar, with turquoise-through-maroon indicating variable-through-conserved. Positions, for which the inferred conservation level was assigned with low confidence, are marked with light yellow. The figure reveals that the functionally important regions on both the DNA and the protein are highly conserved. The run was carried out using PDB code 3COQ and the figure was generated using the PyMol (10) script output by ConSurf.