Conservation, Evolutionary: Difference between revisions
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Eric Martz (talk | contribs) explained the ConSurf process |
Eric Martz (talk | contribs) →The ConSurf Server: polishing |
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==The ConSurf Server== | ==The ConSurf Server== | ||
In brief, the [http://consurf.tau.ac.il ConSurf Server] | The [http://consurf.tau.ac.il ConSurf Server] can calculate and display the conservation pattern for 3D structures '''completely automatically'''. It uses state-of-the-art methods, all of which are published in peer-reviewed journal articles. It also permits considerable customization. For example, the user may submit their own multiple sequence alignment, or phylogenetic tree. I<ref>[[User:Eric Martz]] in January, 2009.</ref> know of no other server with these advantages. | ||
In brief, the [http://consurf.tau.ac.il ConSurf Server] uses the following process by default: | |||
# Obtains the protein sequence for the specified PDB code and chain. | # Obtains the protein sequence for the specified PDB code and chain. | ||
# Gathers closely related sequences from Swiss-Prot (or Uniprot) with a PSI-BLAST search. | # Gathers closely related sequences from Swiss-Prot (or Uniprot) with a PSI-BLAST search. | ||
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# Calculates a conservation score for each amino acid. | # Calculates a conservation score for each amino acid. | ||
# Displays the protein in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]]. | # Displays the protein in interactive 3D, using [[FirstGlance in Jmol]], [[Chimera]], [[PyMOL]], or [[Protein Explorer]]. | ||
==Locating Variable Patches== | ==Locating Variable Patches== | ||
