SERVER FOR THE IDENTIFICATION OF FUNCTIONAL REGIONS IN PROTEINS
ConSurf-DB provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB.
Amino acid sequences similar to each sequence in the PDB were collected and multiply aligned using HMMER and MAFFT, respectively. 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 explicitly into account the phylogenetic relations between the aligned proteins and the stochastic nature of the evolutionary process. Rate4Site assigns a conservation level for each residue using an empirical Bayesian inference. Visual inspection of the conservation patterns on the 3-dimensional structure often enables the identification of key residues that comprise the functionally-important regions of the protein.ConSurf-DB differs from ConSurf in that ConSurf-DB provides pre-calculated conservation profiles, while ConSurf enables considerable flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation.      Last update: November 4th, 2019 on a set of 89,702 protein chains from a total of 108,958 non-redundant protein chains
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Each structure in the PDB is represented by a 4 character alphanumeric identifier, assigned upon its deposition. For example, 1bxl and 1d66 are identification codes for PDB entries for Bcl-Xl / Bak complex and Gal4 (Residues 1 - 65) complex with 19mer DNA, respectively. More on PDB ID...
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ConSurf-DB calculation was preformed for up to 300 homologues with a maximum sequence identity cutoff of 95%