GREEN - A PROGRAM PACKAGE FOR DOCKING STUDIES IN RATIONAL DRUG DESIGN

A program package, GREEN, has been developed that enables docking stud ies between ligand molecules and a protein molecule. Based on the stru cture of the protein molecule, the physical and chemical environment o f the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of th e protein-ligand interaction energy, as well as for the graphical repr esentation of the binding-site environment. The interactive docking op eration is facilitated by various built-in functions, such as energy m inimization, energy contribution analysis and logging of the manipulat ion trajectory. Interactive modeling functions are incorporated for de signing new ligand molecules while considering the binding-site enviro nment and the protein-ligand interaction. As an example of the applica tion of GREEN, a docking study is presented on the complex between try psin and a synthetic trypsin, inhibitor. The program package will be u seful for rational drug design, based on the 3D structure of the targe t protein.