Molecular modeling is a process to predict the structure of a molecule in the absence of wet-lab-based methods. This is a computational prediction process and is often used as a starting point for bench works. There are different algorithms available for the purpose with varying degrees of accuracies. In general, the main focus of the work is directed toward building the structures of biological macromolecules or their complexes. In this review the basic principle of methods of molecular modeling will be reviewed. A special emphasis will be given on thermodynamic aspects of molecular interactions involved in the process of building of the models. The flowchart of the method will be provided. Finally, the algorithm behind some of the popular modeling tools will be analyzed. The readers of the article may gain some first-hand knowledge of the process, which they might use for their computational experimentations.