Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) →Locating Conserved Patches: Added Caveat |
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==Locating Conserved Patches== | ==Locating Conserved Patches== | ||
Patches of highly conserved residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. These can be readily identified and visualized automatically with the [http://consurf.tau.ac.il ConSurf Server], provided a sufficient number of related protein sequences are in the Uniprot database. Before submitting a custom job request to the [http://consurf.tau.ac.il ConSurf Server], check out your [[PDB code]] at [http://consurfdb.tau.ac.il ConSurfDB], a database of precalculated conservation levels for most chains in the [[Protein Data Bank]]. | Patches of highly conserved residues on the surface of a protein molecular structure are good candidates for [[Site | functional sites]]. These can be readily identified and visualized automatically with the [http://consurf.tau.ac.il ConSurf Server], provided a sufficient number of related protein sequences are in the Uniprot database. Before submitting a custom job request to the [http://consurf.tau.ac.il ConSurf Server], check out your [[PDB code]] at [http://consurfdb.tau.ac.il ConSurfDB], a database of precalculated conservation levels for most chains in the [[Protein Data Bank]]. | ||
==Caveat== | |||
This caveat applies only to molecules that contain chains with different sequences. The conservation colors shown in Proteopedia's ''Evolutionary Conservation'' scenes do not indicate the same levels of conservation for chains of different sequences. This is because [http://consurfdb.tau.ac.il ConSurfDB] calculates conservation levels independently for each sequence-different chain, and the levels are relative to the multiple sequence alignment constructed for each sequence-independent chain. | |||
In Proteopedia's ''Evolutionary Conservation'' scenes, we have chosen to color all the chains in the molecule at once. This gives a potentially useful overview, but can be misleading unless one realizes that a given conservation color, in two sequence-different chains, does not mean exactly the same level of conservation. In contrast to Proteopedia's ''Evolutionary Conservation'' scenes, ConSurfDB and ConSurf Server apply conservation level colors to only one chain sequence at a time, thereby avoiding this possible confusion. | |||
==The ConSurf Server== | ==The ConSurf Server== | ||
