Expressive Visualization of Protein Complexes
- Project Identification
- Project Period
- 3/2016 - 12/2018
- Investor / Pogramme / Project type
- Masaryk University
- MU Faculty or unit
- Faculty of Informatics
- Other MU Faculty/Unit
- Faculty of Science
Understanding the molecular machinery of proteins is a basic knowledge that contributes to advances in medicine, pharmaceutics, but also agriculture and even energy sectors. The ultimate goal of proteomic research is to describe functions of all proteins and their complexes in cellular space and life time. Protein interaction patterns are, however, very complex and revealing these is a challenging and time-consuming scientific process. One of the typical tasks of biochemists is to search for appropriate contact zones on the protein surfaces which play a crucial role in mutual interaction between these proteins. This project aims to aid the biochemists with new visualization techniques to enhance the searching for the most biologically relevant contact zones. We will develop novel visualization methods, using different focus and context techniques, specialized visualizations, and their combination to enable the users to explore the contact zones more intuitively. Moreover, the proposed visualizations will serve for mutual comparison and classification of different candidate pairs of contact zones. The ultimate goal is to design and implement a tool enabling to study spatial abstractions of proteins and their possible contact zones. These abstractions are reaching from 1D sequential representation to flattened 2D and newly designed 3D representations.
All proposed techniques will be designed in tight cooperation with the proteomics domain experts who will intensively test these new techniques using their previously and newly acquired experimental data. Particularly, using newly developed methods, biochemists will design new experiments to characterize binary protein-protein interactions between SMC5/6 complex subunits. Our experimental data and new visualization tool integrating the proposed techniques will enable us to reconstruct the architecture of the SMC5/6 complexes and model their dynamics. Moreover, the visualization tool will be provided to the biochemical community worldwide for applications to any protein complexes.