ConSurfDB vs. ConSurf: Difference between revisions
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If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest. | If the list includes proteins of functions that differ from that of the protein of interest, that tends to obscure patches of conservation that exist among proteins with the same function as the query protein of interest. | ||
====Example==== | ====Example With Multiple Functions==== | ||
[[2vaa]] is a [[major histocompatibility complex]] '''class I''' protein (MHC I). ConSurfDB used 300 sequences in its calculation, and the MSA had an '''APD of 1.63'''. Starting about halfway down the list of sequence is the first '''MHC II''' protein, which has a different function. Early in the list is the first of 14 sequences for hemochromatosis proteins (unrelated in function). The list includes 62 "Ig-like domain-containing" proteins of unknown function. The inclusion of these and many other sequences for proteins with functions that differ from the query will obscure conservation of residues critical for the specific functions of MHC I proteins. Therefore, you may prefer to run a ConSurf job in which you <!--limit the MSA to MHC I proteins by manual selection--> limit the APD to a value below 1.0. [[#Examples|See such examples below]]. | [[2vaa]] is a [[major histocompatibility complex]] '''class I''' protein (MHC I). ConSurfDB used 300 sequences in its calculation, and the MSA had an '''APD of 1.63'''. Starting about halfway down the list of sequence is the first '''MHC II''' protein, which has a different function. Early in the list is the first of 14 sequences for hemochromatosis proteins (unrelated in function). The list includes 62 "Ig-like domain-containing" proteins of unknown function. The inclusion of these and many other sequences for proteins with functions that differ from the query will obscure conservation of residues critical for the specific functions of MHC I proteins. Therefore, you may prefer to run a ConSurf job in which you <!--limit the MSA to MHC I proteins by manual selection--> limit the APD to a value below 1.0. [[#Examples|See such examples below]]. | ||
