Tree Diagram Representation of  Unfolded Protein Tunnels

Abstract

In protein dynamics, it is important to explore the accessibility of the reaction site of the protein over time. Reaction site inside the protein is usually approachable by the protein tunnel. In the paper is described a 2D representation of the tunnel, which is a result of a parametrization process of 3D mesh representation into 2 parameters (first parameter samples tunnel along the centerline, the second samples tunnel around it). Usually, protein contains multiple tunnels and several of them share the same parts, which forms a tree-like structure of the tunnels. Overview insight into the shape and composition of multiple tunnels would be beneficial for the biochemist to explore the protein properties and its evolution over time.

Context

This project is part of an ongoing research collaboration between the Masaryk University in Brno, Czech Republic. The project is a follow-up to the research described in the following paper [1].

Assignment

In this project, you will program new way of visualizing a 3D tree-like structure of protein tunnels by transformation to a 2D tree diagram representation. The idea is to get an overview of the compositions of several tunnels in protein in one view.

Requirements

Good programming skills and familiarity with C# and Unity3D are an advantage. No biology background is required.

References

• [1] Kolesar et al. “Unfolding and Interactive Exploration of Protein Tunnels and their Dynamics”, In VCBM,  pp 1-10, 2016, http://www.ii.uib.no/vis/publications/publication/2016/Kolesar-2016-VCBM
• [2] Borkin et al., “Evaluation of Artery Visualizations for Heart Disease Diagnosis”, IEEE Transactions on Visualization and Computer Graphics 17, 12 (December 2011), pp 2479-2488, http://www.eecs.harvard.edu/~kgajos/papers/2011/borkin11-infoviz.pdf

Suitability

• INF219 & INF319

Contact

For more information please contact Jan Byška (jan.byska@gmail.com).