Conservation, Evolutionary: Difference between revisions

The ConSurf DataBase server, [http://consurfdb.tau.ac.il ConSurf-DB], pre-calculates conservation levels for each amino acid in every protein chain in the [[Protein Data Bank]]<ref>PMID: 18971256</ref>. It went into service in 2008. The amino acid sequence of each protein chain is submitted to PSI-BLAST<ref>PSI-BLAST (Position Specific Iteration-BLAST) is an extension of the Basic Local Alignment Search Tool (BLAST) that is more sensitive at finding distantly related sequences. See [http://en.wikipedia.org/wiki/PSI-BLAST PSI-BLAST at Wikipedia] and [http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html PSI-BLAST at NCBI].</ref> for collection of related sequences. The sequences gathered with PSI-BLAST are then filtered using a scheme that attempts a balance between limiting the sequences to close homologues, and including distant sequences that do not share structure or function. The filtered sequence set is multiply aligned with MUSCLE (a multiple sequence alignment algorithm that out-performs CLUSTALW).