The educational publication, written by scientists from Germany, France and Switzerland with extensive pedagogical practice, discusses the main methods of molecular modeling and drug design - a rapidly developing field of modern computer chemistry. Theoretical foundations of modeling the spatial structure of small molecules and methods of constructing dependencies of biological activity on the spatial structure (based on 3D-QSAR), principles of modeling the structure of protein molecules, methods of molecular docking and virtual screening, approaches to choosing a biomarking are presented. Examples of simulations of dopamine D3 receptor antagonists are given. For undergraduate and graduate students, as well as researchers working in the fields of molecular modeling, bio- and chemoinformatics, nanotechnology and the search for new drugs.