The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations. It uses modern software engineering techniques (object-oriented design, a high-level language) to overcome limitations associated with the large monolithic simulation programs that are commonly used for biomolecules. Its principal advantages are (1) easy extension and combination with other libraries due to modular library design; (2) a single high-level general-purpose programming language (Python) is used for library implementation as well as for application scripts; (3) use of documented and machine-independent formats for all data files; and (4) interfaces to other simulation and visualization programs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 79–85, 2000