Cavities are crucial for interactions of proteins with other molecules. While a variety of different cavity types exists, tunnels, in particular, play an important role, as they enable a ligand to deeply enter the active site of a protein where chemical reactions can undergo. Consequently, domain scientists are interested in understanding properties relevant for binding interactions inside molecular tunnels. Unfortunately, when inspecting a 3D representation of the molecule under investigation, tunnels are difficult to analyze due to occlusion issues. Therefore, Malzahn et.al  propose a novel reprojection technique that transforms the 3D structure of a molecule to obtain a 2D representation of the tunnel interior.
This project is part of an ongoing research collaboration between the Masaryk University in Brno, Czech Republic. This thesis project is a follow-up to the research described in a paper .
The goal of this project is to reimplement the method described in  inside a widely used CAVER Analyst  framework.
Good programming skills and familiarity with Java are an advantage. No biology background is required.
-  Malzahn et al. “Protein Tunnel Reprojection for Physico-Chemical Property Analysis” VCBM 2017
-  http://www.caver.cz/
- INF219 & INF319
For more information please contact Jan Byška (firstname.lastname@example.org).