Zinc containing metalloproteinases are important enzymes in many disease processes such as cancer, hypertension and bacterial infections and are important drug targets. This project aims to study the molecular interactions of small molecule inhibitors wit h zinc containing proteins with the aim of accurately predicting experimentally derived inhibition values of the small molecule-protein complexes. The in-house software Sanjeevini will be used to do docking studies of small molecule-Matrix Metalloprotein ases complexes and small molecule- thermolysin like enzyme complexes. Molecular dynamics simulations of the docked protein-ligand complexes followed by a rigorous analysis of the binding free energy estimates will also be done. The result of the project w ill help understanding the selectivity and specificities of these enzymes and aid in the design of novel small molecule inhibitors that may be of clinical significance.