NewProt: A European protein engineering project
Home Partners Contact Project Products Deliverables Restricted
Additional information
Something else
Press release
Legal note

WP 5: Structure analysis and visualisation


To provide an interface for the visualisation of protein structures, predicted and observed mutations, protein-protein and protein-ligand interactions, and other computational results produced by SSP software.


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.

Task 1

YASARA View is a freely available molecular modelling and visualization software that has been distributed by YASARA Biosciences GmbH since 2003 at 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.

Task 2

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 systems (MCSIS).

  The NewProt project is funded by the European Commission within its FP7 Programme, under the thematic area KBBE-2011-5 with contract number 289350.