While many essential computational tasks in drug discovery can now be accomplished with free or open-source components, there is currently no context where such components might be effortlessly combined to carry out complex multi-step procedures in molecular modeling and informatics. The FreeMOL project aims to establish this context by implementing a minimal set of common assumptions that will nucleate the world's first open-source molecular operating environment for drug-discovery.

The open-source, anchoring visualization component, molecular graphics program PyMOL will be used to catalyze the creation of FreeMOL, while FreeMOL components are integrated. However, since FreeMOL is merely a set of assumptions held together with dynamic scripting languages like Python and Perl, PyMOL will eventually be just another interchangeable component in the FreeMOL suite of interoperable tools.

When complete, FreeMOL will contain capabilities comparable to commercial software suites, including molecular visualization, drawing, clean up, energy minimization, dynamics, searching, storage, enumeration, docking, electrostatics, sequence alignment, homology modeling, and so forth. Plus, FreeMOL will serve as an open conduit for integrating diverse commercial software packages, thus eliminating the need for the many redundant integrative development efforts currently ongoing throughout the industry.

As an open-source alternative to commercial software suites, FreeMOL will benefit research in academia and industry by greatly increasing the amount of computational Science, which can be done with minimal expense. Also, by providing competition to commercial packages, FreeMOL will bring about a decrease in price and an increase in the quality of commercial tools.