What's New in ConSurf 3?
- Sequence homologs can be retrieved from Uniprot, as an
- A new Bayesian method of calculating amino acid
is the default.
server now uses the MUSCLE
software as default, in addition to
CLUSTALW, to align the
homologues extracted from the PSI-BLAST output file.MUSCLE
to achieve the highest scores on four alignment accuracy
(relevant to 2004).
- The server can now accept a user-provided phylogenetic tree (in
- ConSurf now indicates amino acids for which the
alignment provided insufficient data for reliable calculation
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 ..).
- 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.
- Insertions into the amino acid numbering sequence, which
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
- 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.
- 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
Examples of downloaded ConSurf job PDB files are provided in FGiJ's Gallery and in
Presentations of ConSurf results can be prepared in a variety of
ways, some new. Instructions are provided for FGiJ
and for PE.
- The new version of Protein Explorer (PE) employed is compatible
with a larger range of browsers
- Protein Explorer's
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
chain, checkboxes appear to control how many are colored by the ConSurf
are available for insufficient data. Seven links at the bottom of the
control panel provide extensive documentation and help, including one, ConSurf
that summarizes the ConSurf job optional parameters and summary
including a link to the on-line results page, and the job run time.
(This information is now recorded in the PDB file itself).
- The new version of Protein Explorer employed has a number of
new generic capabilities (not specific to ConSurf, but can be used
with any ConSurf result):
- Features of the Molecule, a new control panel that
key information in the PDB file header into readable and clickable
(Click More.. at the top of the ConSurf control panel to see
- A new PE Site Map allows you to jump to any control
within PE, as well as to open several other PE resources or external
- A new Undo button undoes the last change to the
- The History feature allows you to preview, and reset
any previous molecular view in the session.
- A powerful new MolSlides
makes it easy to save any molecular view as a slide with a rotatable,
- MolSlides can be imported back into a PE session, thereby
the slides to be edited or new slides to be added to a set. PE's
built-in MolSlide Manager enables text to be added to
and the slides can be reorganized, copied, joined into molecular
comparisons, and more.
- The state of a PE session can be saved and restored. This is
by saving a MolSlide. In a new session, after the MolSlide is imported,
it can be applied to PE.
- Jmol (which works in most
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
requires MDL Chime. But once created, the MolSlides can be viewed in
more browsers and platforms, without running Protein Explorer.
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
- A master list is provided listing all
documentation concerning Protein Explorer's interface to ConSurf.
- PDB files illustrating a range of technical issues are listed
in a new document, ConSurf-PE Validation Tests.
Feedback to Eric