Protein Tunnel Reprojection for Physico-Chemical Property Analysis

Protein Tunnel Reprojection for Physico-Chemical Property Analysis


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 [1] 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 [1].


The goal of this project is to reimplement the method described in [1] inside a widely used CAVER Analyst [2] framework.


Good programming skills and familiarity with Java are an advantage. No biology background is required.



  • INF219 & INF319


For more information please contact Jan Byška (