Large-Scale Analysis of the Ligand Transport and Docking inside of the Protein Tunels

This thesis discusses large-scale analysis of the ligand transport and docking inside of the protein tunnels. Protein-ligand interactions are involved in processes such as cell signalling, transport, metabolism, regulation, gene expression, and enzyme activity. To understand the interaction between these molecules is vitally important for the research for new pharmaceuticals. The procedure of protein-ligand docking involves the following steps: (i) finding the structures of proteins (receptors) and ligands, (ii) identifying ligand binding sites, (iii) considering receptor/ligand flexibility, and (iv) computing interaction energy between the receptor and the ligand. Additional functionality will be implemented to allow CaverWeb to test a complete set of pre-processed drug ligands on a protein, in an effort to enhance the efficiency of the procedure for large sets of ligands, which will allow a much smoother workflow