What's New in ConSurf 3?
- Sequence homologs can be retrieved from Uniprot, as an alternative
- A new Bayesian method of calculating amino acid
is the default.
- 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 ..).
- 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
as well as in the
list of PDB files used for testing.
- The new version of Protein Explorer (PE) employed is compatible
larger range of browsers in Windows.
- 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 ConSurf-processed
chain, checkboxes appear to control how many are colored by the ConSurf results.
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).
- 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):
- Features of the Molecule, a new control panel that converts
key information in the PDB file header into readable and clickable form.
(Click More.. at the top of the ConSurf control panel to see this.)
- A new PE Site Map allows you to jump to any control panel
within PE, as well as to open several other PE resources or external
- A new Undo button undoes the last change to the molecular view.
- The History feature allows you to preview, and reset to,
any previous molecular view in the session.
- A powerful new MolSlides feature
makes it easy to save any molecular view as a slide with a rotatable,
- MolSlides can be imported back into a PE session, thereby enabling
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 MolSlides,
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 done
by saving a MolSlide. In a new session, after the MolSlide is imported,
it can be applied to PE.
- 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
Protein Explorer (PE), all the standard ConSurf controls will appear
automatically. (The ConSurf control panel is now built into PE.)
While displayed in PE, a link ConSurf Job Information will summarize
the job parameters.
Instructions are provided for downloading
and using ConSurf job PDB files.
of downloaded ConSurf job PDB files are provided.
- 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
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.
- Presentations of ConSurf results can be prepared in a variety
of ways, some new.
Instructions are provided.
- It is now relatively easy to change the standard color scheme
used by ConSurf to one of your choosing. See the
for 2VAA among the examples.
Instructions are provided.
- 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 Martz.