DisVis is a software developed in our lab to visualise and quantify the information content of distance restraints between macromolecular complexes. It is open-source and available for download from our Github repository. To facilitate its use, we have developed a web portal for it.
This tutorial demonstrates the use of the DisVis web server. The server makes use of either local resources on our cluster, using the multi-core version of the software, or GPGPU-accelerated grid resources of the EGI to speed up the calculations. It only requires a web browser to work and benefits from the latest developments in the software based on a stable and tested workflow. Next to providing an automated workflow around DisVis, the web server also summarises the DisVis output highlighting relevant information and providing a first overview of the interaction space between the two molecules with images autogenerated in UCSF Chimera.
The case we will be investigating is the interaction between two proteins of the 26S proteasome of S. pombe, PRE5 (UniProtKB: O14250) and PUP2 (UniProtKB: Q9UT97). For this complex seven experimentally determined cross-links (4 ADH & 3 ZL) are available (Leitner et al., 2014). We added two false positive restraints - it is your task to try to identify these! For this, we use DisVis to try to filter out these false positive restraints while assessing the true interaction space between the two chains. We will then use the interaction analysis feature of DisVis that allows for a more complete analysis of the residues putatively involved in the interaction between the two molecules. To do so, we will extract all accessible residues of the two partners, and give the list of residues to DisVis using its interaction analysis feature. Finally, we will show how the restraints can be provided to HADDOCK in order to model the 3D interaction between the 2 partners.