At long last, Protein Explorer (PE) now supports presentations.
For examples, full documentation, and a template with instructions for
creating your own Presentations in PE (PiPEs), go to
proteinexplorer.org
and look for the version supporting presentations.
Two categories of PiPEs exist, each aimed at different audiences.
In both cases, the advantage is that any image in the presentation can be
explored with the full power of Protein Explorer.
Presentations in Protein Explorer I:
Research and Database Communication
Several bioinformatics research groups have expressed interest, but
so far only one has implemented a working server. Because PIPE support
and documentation are still under development, implementation required a close
collaboration between Eric Martz (working on PE) and the research group
in Tel-Aviv. Once full support and documentation for PIPE have been released,
it should be possible to author such resources with little or no
assistance from Martz.
- ConSurf: A server for identification of conserved regions
in proteins by surface mapping of phylogenetic information.
By Fabian Glaser and Nir Ben-Tal (Tel-Aviv Univ., Israel),
Tal Pupko (Inst. Mathematical Statistics, Tokyo Japan),
and Eric Martz (Univ. Massachusetts, USA).
You enter a PDB ID code, or upload atomic coordinates. The server
automatically finds similar sequences, aligns them, constructs a
phylogenetic tree, and colors residues in the 3D protein according to the
resulting conservation scores. The result is displayed in Protein Explorer (PE).
Regions of high conservation are likely to have functional significance.
The left image of enolase was produced by PE's MSA3D using a multiple
protein sequence alignment laboriously constructed by hand.
The right image of enolase was produced by ConSurf merely by specifying
the PDB ID code. Note the good agreement of conserved residues (dark
green and dark purple respectively), which cluster in the catalytic pocket.
Here is
more information on ConSurf vs. MSA3D,
and a transcriptional repressor
example.
Presentations in Protein Explorer II: Educational Tutorials
The presentations below were prepared
before the public release of PE supported presentations.
They employ a now-obsolete format. They remain here for the
historical record, and for those interested in their subject matter.
The publically released and supported format for new PiPEs,
along with example PiPEs, full documentation, and a template for creating
new PiPEs can
be found at proteinexplorer.org.
These presentations were created by students in
Macromolecular Visualization Lab (Microbiology 597V).
These tutorials are presented within
Protein Explorer. This means that any
image in the presentation can be explored with the full power
of Protein Explorer if desired.
The presentation interface within Protein Explorer is currently
under development. It will not be generally available until it is
completed, at which time a link to the documentation and download
site will be placed here. Because it was in a partially developed
state when the tutorials below were developed, they have some
instability and limitations. It is best to allow plenty of time
after pressing a button for the javascript to catch up before
pressing another button. If it crashes, close it, start
again and be more patient between buttons!
2000 version of Protein Explorer with latest (fall 2000)
under-development version of Presentations in Protein Explorer (PIPE).
This version of PIPE adds pop-up details, presentation controls for details,
font size, and documentation for the controls.
It has 3 modes: one person, audience (for projection),
and development. It operates in PE 1.72-beta. An alpha-test version of
a script recorder was used by the students in authoring their presentations,
but because it is in a rough state, the script recorder is not included
in the copies here.
Unless otherwise indicated, these require an older version of
Chime, (2.0.3 for Windows), which is
available from MDL.)
The presentations below are offered primarily for their top-quality content.
Both of the presentations below have benefited from a great deal of effort
by these students beyond what was
required in the course.
(These operate in PE 1.1-beta, fall 1999, in the fall 1999
under-development version of Presentations in Protein Explorer.
Unless otherwise indicated, these require an older version of
Chime, (2.0.3 for Windows), which is
available from MDL.)