Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
Eric Martz (talk | contribs) →The ConSurf-DB Mechanism: describing ConSurf-DB Mechanism |
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#Rate4Site then calculates an evolutionary rate for each position in the MSA using a [http://en.wikipedia.org/wiki/Bayesian_inference Bayesian] approach shown by the ConSurf team to be superior<ref>PMID: 15201400</ref>. "The amino acid evolution is traced using the JTT<ref> PMID: 1633570</ref> substitution model. High evolutionary rate represents a variable position while low rate represents an evolutionarily conserved position."<ref name="consurfdb" /> | #Rate4Site then calculates an evolutionary rate for each position in the MSA using a [http://en.wikipedia.org/wiki/Bayesian_inference Bayesian] approach shown by the ConSurf team to be superior<ref>PMID: 15201400</ref>. "The amino acid evolution is traced using the JTT<ref> PMID: 1633570</ref> substitution model. High evolutionary rate represents a variable position while low rate represents an evolutionarily conserved position."<ref name="consurfdb" /> | ||
#"The conservation scores are normalized so that the average over all residues is zero, and the standard deviation is one."<ref name="consurfdb" /> Thus, '''conservation scores are relative, not absolute''' and comparing them between different protein families might be misleading (see [[#Caveat|Caveat]] above). | #"The conservation scores are normalized so that the average over all residues is zero, and the standard deviation is one."<ref name="consurfdb" /> Thus, '''conservation scores are relative, not absolute''' and comparing them between different protein families might be misleading (see [[#Caveat|Caveat]] above). | ||
#The normalized conservation scores are then | #The normalized conservation scores are then divided into nine levels from 1 (highly variable) to 9 (highly conserved). | ||
#Colors mapped to the nine conservation levels, from turquoise (1) to burgandy (9) are applied to the 3D protein structure visualized in [[FirstGlance in Jmol]]. | #Colors mapped to the nine conservation levels, from turquoise (1) to burgandy (9) are applied to the 3D protein structure visualized in [[FirstGlance in Jmol]]. | ||
