Author: Stefan

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

Abstract 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

Abstract Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behaviour. Studying these factors helps the biochemists and biologists to better understand the protein behaviour and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other