MOE (Molecular Operating Environment) 

MOE is a comprehensive software system for Life Science. MOE is a combined Applications Environment and Methodology Development Platform that integrates visualization, simulation and application development in one package. MOE contains a broad base of scientific applications for general modeling, drug design, homology modeling, library design. MOE is licensed by the School of Chemical Sciences for research use and is part of the Scientific Software Program.

The Chemical Computing Group (CCG) also provides the School of Chemical Sciences with 60 teaching licenses for MOE each semester at no cost.  

MOE Tutorial

Tutorial - Introduction to molecular mechanics with MOE: Why does GFP need a beta-barrel shell?

Schrodinger

Schrodinger is a state-of-the-art chemical simulation software used for a variety of modeling, analysis and computational tasks such as drug discovery and optimization, molecular simulations of chemical systems, and molecule design.  It is used in fields such as pharmacology and biotechnology research.  The Schrodinger Suite is licensed by the School of Chemical Sciences and is part of the Scientific Software Program.