What's New in ConSurf 3?
  1. Sequence homologs can be retrieved from Uniprot, as an alternative to SWISS-PROT.

  2. A new Bayesian method of calculating amino acid conservation scores is the default.

  3. The server now uses the MUSCLE software as default, in addition to  CLUSTALW, to align the homologues extracted from the PSI-BLAST output file.MUSCLE was shown to  achieve the highest scores on four alignment accuracy benchmarks (relevant to 2004).

  4. The server can now accept a user-provided phylogenetic tree (in Newick format).

  5. ConSurf now indicates amino acids for which the multiple sequence alignment provided insufficient data for reliable calculation of conservation grades. These amino acids are colored yellow by default. The calculated (but generally unreliable) grades for these amino acids can be displayed if desired. (More ..).

  6. A graphical representation of the phylogenetic tree is now available,  using the Hickory java applet; part of the Hickory package (which also includes a stand-alone application), the applet provides an interactive tool for viewing and manipulating phylogenetic trees. The applet is web-based, and so no download or installation is required by the user.

  7. Insertions into the amino acid numbering sequence, which were not handled correctly in ConSurf 2, are now handled correctly. Some such cases are included in the examples as well as in the list of PDB files used for testing.

  8. Beginning September, 2006, results can be viewed in FirstGlance in Jmol as an alternative to Protein Explorer. Unlike Protein Explorer, which works only in MS Windows or Mac Classic, FirstGlance in Jmol also works in Mac OSX (Safari) and linux (Mozilla Firefox). Pros and cons for each viewer.

  9. The results of each ConSurf job can now be saved as a single PDB file. This file contains the conservation grades and color scheme, and the parameters used in the job. When displayed in FirstGlance in Jmol (FGiJ) or Protein Explorer (PE), all the standard ConSurf controls will appear automatically. A link to ConSurf Job Information will summarize the job parameters. Instructions are provided for downloading and using ConSurf job PDB files for FGiJ and for PE. Examples of downloaded ConSurf job PDB files are provided in FGiJ's Gallery and in PE.

  10. Presentations of ConSurf results can be prepared in a variety of ways, some new. Instructions are provided for FGiJ and for PE.

  11. The new version of Protein Explorer (PE) employed is compatible with a larger range of browsers in Windows.

  12. Protein Explorer's ConSurf control panel has many enhancements. More information about the model being viewed is accessible in one click ("More.." at the top). Each color in the color key is now a toggle to hide or show amino acids at that level of conservation. When the mouse touches a color grade in the color key (touches, not clicks), a message appears showing the number of residues having that grade. When there are multiple chains identical in sequence with the ConSurf-processed chain, checkboxes appear to control how many are colored by the ConSurf results. Multiple displays are available for insufficient data. Seven links at the bottom of the control panel provide extensive documentation and help, including one, ConSurf Job Information, that summarizes the ConSurf job optional parameters and summary results, including a link to the on-line results page, and the job run time. (This information is now recorded in the PDB file itself).

  13. The new version of Protein Explorer employed has a number of major new generic capabilities (not specific to ConSurf, but can be used with any ConSurf result):
  14. Jmol (which works in most popular browsers, in Mac OSX and linux as well as windows) can be used to present ConSurf results by saving them into MolSlides. Here is an Example of ConSurf results in Jmol Note that creating MolSlides in Jmol requires Protein Explorer, which in turn requires MDL Chime. But once created, the MolSlides can be viewed in more browsers and platforms, without running Protein Explorer. (More..)

  15. It is now relatively easy to change the standard color scheme used by ConSurf to one of your choosing. See the demonstration for 2VAA in FGiJ's Gallery and in PE. Instructions are provided.


  16. A master list is provided listing all documentation concerning Protein Explorer's interface to ConSurf.

  17. PDB files illustrating a range of technical issues are listed in a new document, ConSurf-PE Validation Tests.

Feedback to Eric Martz.