[Molvis-list] Announcing ConSurf 3

emartz at nre.umass.edu emartz at nre.umass.edu
Fri Jun 23 07:21:41 EDT 2006

The ConSurf Server (http://consurf.tau.ac.il) calculates the level of
evolutionary conservation for each amino acid in a protein, entirely
automatically, and displays the 3D structure colored by conservation grades. It
has been available since fall 2002.

ConSurf version 3 has just been released. New capabilities include:

 - An improved Bayesian method for calculating conservation scores.
 - Improved multiple sequence alignments via MUSCLE.
 - Retrieval of sequence homologs from either SWISS-PROT or Uniprot.
 - Residues with insufficient data to calculate a reliable conservation grade
are now indicated.
 - Users who wish can upload their own phylogenetic trees (or, as before, their
own multiple sequence alignments or atomic coordinates).

 - Results can be downloaded as a single (modified PDB) file, and redisplayed in
Protein Explorer 2.78 or later (http://proteinexplorer.org) even after the
results have been deleted from the ConSurf server. Saved results can be
displayed off-line with a downloaded copy of Protein Explorer 2.78 or later.

 - Results, which are displayed in Protein Explorer, can now be viewed in a
wider range of browsers on Windows (Firefox, Netscape 7.2 or 4.8, Mozilla,
Internet Explorer).
 - Intel Mac OSX users can view results in a Windows subsystem (see parallels.com).
 - PPC Mac OSX users need Classic in order to view results in Protein Explorer.

 - Selected views of ConSurf results can be saved in MolSlides in Jmol (as well
as Chime). MolSlides have rotatable, zoomable molecular views, and can be viewed
without Protein Explorer. MolSlides in Jmol can be viewed in most popular
browsers and platforms, including Safari/OSX and Mozilla/linux. An example of
ConSurf views in Jmol MolSlides is here:

A more detailed list of what is new in ConSurf 3 is here:

The ConSurf server was developed by Fabian Glaser, Yossi Rosenberg, Tal Pupko,
Itay Mayrose, and Meytal Landau with Nir Ben-Tal (Tel-Aviv University, Israel)
in collaboration with Eric Martz (University of Massachusetts). 


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