Abstract
Proteins are essential for functioning of all living organisms and studying their inner structure and functions has been of a high importance. Many studies concentrated on detection of various inner structures inside macromolecules (e.g. tunnels, channels, pores) which play an essential role in the functioning of a large number of proteins. Here we present a novel approach to a detection of intramolecular tunnels. These pathways may facilitate the transport of reaction intermediates among buried active sites. The results obtained by the proposed algorithm were compared to intramolecular tunnels whose presence in given structures is already known. The algorithm is able to also identify other inner structures, such as channels or pores.