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.
Provides simple and universal access to interpret protein structures and sequences in light of their evolutionary variations and divergences. UET is a repository of pre-computed evolutionary trace (ET) analyses performed on the protein structure databank (PDB). UET can be accessed via a web interface using a given protein structure to retrieve an ET ranking of sequence positions and to identify functionally important regions in that structure. In UET, seamless integration of structure and phylogenetic tree viewers in the web browser means that a user can examine protein structures and sequences with their ET analyses, without any prior software installation. It also avoids access, update and digital signing issues that often plague viewers based on Java applets that run on browsers.