GlaxoSmithKline
R&D
&
the Swiss Institute of Bioinformatics
present
Deep
View
Swiss-PdbViewer
by
Nicolas Guex , Alexandre Diemand
, Manuel C. Peitsch
, & Torsten Schwede
Description
Swiss-PdbViewer
is an application that provides a user friendly interface allowing to
analyze several proteins at the same time. The proteins can be superimposed
in order to deduce structural alignments and compare their active sites
or any other relevant parts. Amino acid mutations, H-bonds, angles and
distances between atoms are easy to obtain thanks to the intuitive graphic
and menu interface.
Moreover,
Swiss-PdbViewer is tightly linked to
Swiss-Model, an automated homology modeling server developed within
the Swiss Institute of Bioinformatics
(SIB) in collaboration between GlaxoSmithKline
R&D and the Structural
Bioinformatics Group at the Biozentrum in Basel.
Working with
these two programs greatly reduces the amount of work necessary to generate
models, as it is possible to thread a protein primary sequence onto a
3D template and get an immediate feedback of how well the threaded protein
will be accepted by the reference structure before submitting a request
to build missing loops and refine sidechain packing.
Swiss-PdbViewer
can also read electron density maps, and provides various tools to build
into the density. In addition, various modeling tools are integrated and
command files for popular energy minimization packages can be generated.
Finally,
as a special bonus, POV-Ray scenes can be generated from the current view
in order to make stunning ray-traced quality images. An example can be
found here .
[last
modified: 6. June. 2003 by T.S.]
|