Conservation, Evolutionary: Difference between revisions
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Briefly, ConSurf-DB gathers sequences similar to that of the protein in question, then constructs a multiple sequence alignment, and analyses it for sequence positions that are conserved (have lower than average differences between sequences) and that are variable (have higher than average differences between sequences). Each amino acid is assigned a conservation score and corresponding color in Proteopedia's interactive 3D molecular scene. | Briefly, ConSurf-DB gathers sequences similar to that of the protein in question, then constructs a multiple sequence alignment, and analyses it for sequence positions that are conserved (have lower than average differences between sequences) and that are variable (have higher than average differences between sequences). Each amino acid is assigned a conservation score and corresponding color in Proteopedia's interactive 3D molecular scene. | ||
ConSurf-DB's analysis is done with sophisticated, published, peer-reviewed, state of the art methods. A more detailed overview of the [[# | ConSurf-DB's analysis is done with sophisticated, published, peer-reviewed, state of the art methods. A more detailed overview of the [[ConSurfDB_vs._ConSurf#ConSurf-DB_Process|process employed by ConSurf-DB]] is available. Proteopedia's built-in display of ConSurf-DB results is a good place to start looking for conserved patches. | ||
However, as explained [[#ConSurf-DB Usually Hides Some Functional Sites|below]], ConSurf-DB usually does not show all the conserved patches present in proteins with the same function. Therefore, you may wish to extend your analysis of conservation by limiting the analysis to proteins of one function, using the ConSurf Server, as explained [[#Limiting Conservation Analysis to Proteins of a Single Function|below]]. The results of such an analysis can be displayed in a molecular scene in Proteopedia. See below for [[#Examples|Examples]] and [[#How to Insert a ConSurf Result Into a Proteopedia Green Link|Instructions]]. | However, as explained [[#ConSurf-DB Usually Hides Some Functional Sites|below]], ConSurf-DB usually does not show all the conserved patches present in proteins with the same function. Therefore, you may wish to extend your analysis of conservation by limiting the analysis to proteins of one function, using the ConSurf Server, as explained [[#Limiting Conservation Analysis to Proteins of a Single Function|below]]. The results of such an analysis can be displayed in a molecular scene in Proteopedia. See below for [[#Examples|Examples]] and [[#How to Insert a ConSurf Result Into a Proteopedia Green Link|Instructions]]. | ||
