The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures

Abstract

ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The algorithm takes into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process explicitly. Rate4Site assigns a conservation level for each position in the multiple sequence alignment using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3D structure often enables the identification of key residues that comprise the functionally important regions of the protein. The repository is updated with the latest PDB entries on a monthly basis and will be rebuilt annually. ConSurf-DB is available online at http://consurfdb.tau.ac.il/

Figure 1.

Cytochrome c. (A) The conservation coloring profile from the ConSurf-DB repository, mapped onto a space-filling representation of the protein. The conservation coloring scale is shown below. The HEME group, in stick representation, is colored green. (B) The same view as calculated by the ConSurf server using default parameters.