CAVER Viewer - the explorer of behaviour of tunnels in proteins

Abstract

Protein exploration in order to discover new medication has been the principal aim of biochemists. In combination with informatics the solution of this task can be faster, more accurate and also more intuitive and straightforward in comparison with traditional methods. Our CAVER Viewer application allows the exploration of protein structures and the visualization of results. It enables to find certain paths from the outer space around the molecule to the specific site inside the protein called the active site. The existence of these important paths (also called tunnels or channels) is crucial in the process of transferring some small molecule of substrate into this active site. Namely, the substrate enters the active site via these precomputed tunnels. There the chemical reaction between the substrate and protein can undergo. The product of this reaction can form the basis of a new medication. This poster describes the key aim of our research in the field of protein visualization, when we have to visualize the protein dynamics - movements of the molecule as well as the behaviour of its tunnels in time space.