What is ConSurf?
ConSurf is a widely used tool for revealing functional regions in macromolecules by analysing the evolutionary dynamics of amino/nucleic acids substitutions among homologous sequences (1–4).
What is ConSurf used for?
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 …
What data do you need to calculate a conservation score?
Conservation scores are calculated per base, indicating how many species in a given multiple alignment match at each locus.
What is the PDB code?
Every molecular model (atomic coordinate file) in the Protein Data Bank (PDB) has a unique accession or identification code. These codes are always 4 characters in length. Plans for an expanded identification code system that handle more entries have been announced.
What is a Psi Blast?
Position-Specific Iterative (PSI)-BLAST is a protein sequence profile search method that builds off the alignments generated by a run of the BLASTp program. This process is iteratively continued until desired or until convergence, i.e., the state where no new sequences are detected above the defined threshold.
How do I find my PDB?
Every released entry in the PDB has an automatically-generated page in Proteopedia. To find it, simply enter the PDB code in the search slot found at the left of this (and every) page in Proteopedia.
What is the purpose of the consurf server?
The ConSurf server [1] 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.
Which is the main algorithm behind ” consurf “?
Rate4Site – is the main algorithm behind ConSurf. Installation : The sources are already in the folder 3rd party software. ConSurf requires the fast and slow versions. In order to obtain both of them simply run rate4site_build.sh script: ClustalW – please download from EBI; ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
How is the evolutionary rate estimated in consurf?
In ConSurf, the evolutionary rate is estimated based on the evolutionary relatedness between the protein (DNA/RNA) and its homologues and considering the similarity between amino (nucleic) acids as reflected in the substitutions matrix [2,3].
