PhD position in Visualization and visual analysis of protein-protein interactions

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.

In this project aims to aid the biochemists with new visualization techniques to enhance the searching for the most biologically relevant contact zones. We are developing 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 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 are designed in tight cooperation with the proteomics domain experts who intensively test these new techniques using their previously and newly acquired experimental data.

Within this project, you will focus on the following topics:
1. How to represent the information about the contact zones between interacting proteins in the most intuitive and comprehensible way.
2. How to compare contact zones of different possible configurations.7
3. How to extend newly proposed techniques for contact zones between two proteins to multiprotein interactions.

This project runs in collaboration with proteomics experts from the Masaryk University in Brno.

The successful candidate is supposed to have his or her degree in Computer Graphics, with some experience in visualization.

Required knowledge: Java, OpenGL

The position is funded from the project of the grant agency of the Masaryk University.
Informal inquiries can be made to Dr. Barbora Kozlikova ([Email Address Removed]) with a copy of your CV and cover letter.