How to see conserved regions: Difference between revisions
Eric Martz (talk | contribs) New page: Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation. |
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Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see [[Introduction to Evolutionary Conservation]]. | Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see [[Introduction to Evolutionary Conservation]]. | ||
==Conservation in Proteopedia== | |||
Most molecules in Proteopedia, on pages titled with a [[PDB code]], have an ''Evolutionary Conservation'' line below the molecule. Clicking on '''<nowiki>[show]</nowiki>''' in this line will color the molecule by evolutionary conservation, as calculated by [[ConSurfDB_vs._ConSurf|ConSurfDB]]. | |||
If the molecule of interest lacks the ''Evolutionary Conservation'' line below the molecule, you can calculate it yourself at the ConSurf Server. [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Here are instructions.]] When you get the result, there will be a link for showing that result in [[FirstGlance in Jmol]]. | |||
You can also [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|show ConSurf-colored molecules with green links in Proteopedia]]. | |||
==Conservation in FirstGlance== | |||
You might wish to explore a conservation-colored molecule in [[FirstGlance in Jmol|FirstGlance]] so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons. | |||
#Enter the [[PDB code]] in the search slot in Proteopedia. | |||
#At the page title with the PDB code, click on '''<nowiki>[show]</nowiki>''' in the line labeled ''Evolutionary Conservation'' beneath the molecule. (If there is no such line, see below.) | |||
#The ''Evolutionary Conservation'' section is now expanded. Click on the link ''Complete Results at ConSurfDB''. | |||
#At ConSurfDB, click on the button for the chain of interest under ''View 3D structure colored by conservation in FirstGlance in Jmol''. (You can only see one chain at a time at ConSurfDB. [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|Here is the reason.]]) | |||
Revision as of 01:01, 2 October 2012
Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation.
Conservation in ProteopediaConservation in Proteopedia
Most molecules in Proteopedia, on pages titled with a PDB code, have an Evolutionary Conservation line below the molecule. Clicking on [show] in this line will color the molecule by evolutionary conservation, as calculated by ConSurfDB.
If the molecule of interest lacks the Evolutionary Conservation line below the molecule, you can calculate it yourself at the ConSurf Server. Here are instructions. When you get the result, there will be a link for showing that result in FirstGlance in Jmol.
You can also show ConSurf-colored molecules with green links in Proteopedia.
Conservation in FirstGlanceConservation in FirstGlance
You might wish to explore a conservation-colored molecule in FirstGlance so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons.
- Enter the PDB code in the search slot in Proteopedia.
- At the page title with the PDB code, click on [show] in the line labeled Evolutionary Conservation beneath the molecule. (If there is no such line, see below.)
- The Evolutionary Conservation section is now expanded. Click on the link Complete Results at ConSurfDB.
- At ConSurfDB, click on the button for the chain of interest under View 3D structure colored by conservation in FirstGlance in Jmol. (You can only see one chain at a time at ConSurfDB. Here is the reason.)