This WP logically separates into two tasks. First, the incorporation of
YASARA View functionality in the SSP, and second, the access to SSP
functionality from within YASARA View.
YASARA View is a freely available molecular modelling and visualization
software that has been distributed by YASARA Biosciences GmbH since 2003
at www.yasara.com. There are currently >20000 registered users, many of
whom decided to support YASARA development by switching to one of the
higher (commercial) stages with additional features (like molecular
simulations). For the purpose of the SSP, the free YASARA View provides
all the functions needed, and YASARA Biosciences GmbH has granted
permission to include the software in any virtual machine distributed
by the NewProt project.
The SSP will often need to visualize residues coloured by characteristics
such as mutability, conservation, or involvement in protein-protein and
protein-ligand contacts. While this could in principle be achieved with
any molecular graphics software, the SSP will also require advanced
visualisations that extend far beyond simple colouring and styling.
These will include side-chain rotamers, cavities, surfaces, electrostatic
potentials etcetera. In Task 1, we will develop open source YASARA
scripts that create these visualizations on the fly, and output them
either as ray-traced images (for display on the SSP website) or as
annotated YASARA scene files. When the user clicks on such a hyperlinked
YASARA scene, it will be opened in his/her local YASARA View to provide
a fully immersive, photorealistic environment for detailed analysis.
Some of the results obtained from the various SSP software packages may
have to be processed or converted before they can be visualized. This
will hold mainly for WHAT IF results. Partner CMBI will, with advice
from partner YAS, perform this task. The order in which WHAT IF
calculations will be made YASARA scene friendly will be determined
by the (experimental) partners who will use the WHAT IF facilities at the SSP.
As mentioned in the introduction, the SSP will not only provide
interactive access via a web browser, but also support automatic
access via a SOAP interface. To demonstrate the use of this interface,
partner YASARA will develop an open source Python plug-in for YASARA
View, that integrates SSP functionality directly into the user interface.
This permits users to query the SSP from within YASARA View, while
analyzing their protein structure of interest, without having to open a
browser window in parallel. This principle has already been successfully
applied to include a large number of external web services into YASARA
View: structural alignments using CE, MultiProt, and SHEBA, mutant
analysis with FoldX, the PDBFINDER-II database, visualization of conserved
surface residues with ConSurf, or molecular class-specific information