Hypercube is a scientific software company, incorporated in 1985, specializing in molecular modeling software. 

The company has origins associated with the University of loo and is located in Waterloo, Ontario, Canada, adjacent to the university. Many of its employees have had or continue to have ties with the university.

Its founder and current President and CEO is Neil S. Ostlund. Dr. Ostlund has held tenured academic faculty positions in the different disciplines of chemistry and computer science at different times at different universities in different countries. Most recently he was a faculty member and the director of the computer architecture lab in the computer science department of the University of Waterloo. In 1987, Dr. Ostlund left the University of Waterloo to work full-time for Hypercube, hiring its first full-time employees.

The first phase of Hypercube, Inc.'s existence involved contracting for Intel in association with Intel's development of the first commercial highly-parallel computer, the Intel iPSC hypercube computer. This is the origin of the company's name. Subsequent to this, Intel and Hypercube cooperated in the development and marketing of molecular modeling software for the commercial Intel iPSC.

A second phase of Hypercube, Inc's history involved the internal develpment of a turn-key molecular modeling "instrument" called a Chemputer consisting of a PC integrated with a parallel processing sub-system of Transputers running HyperChem, 1. A small number of these machines were build and sold to institutions such as NIH, University of California, and University of North Carolina.

A Third phase of Hypercube, Inc.'s history involved a joint venture with Autodesk, Inc., initiated in 1990. Autodesk acquired an exclusive license to manufacture, market, and sell HyperChem with Hypercube doing all development and technical support for the products. The first Autodesk product, HyperChem Release 2, was shipped in March of 1992. Release 3 was shipped in April of 1993.

In January of 1994, Hypercube recovered its license from Autodesk and brought all control for HyperChem and related products in-house. Hypercube, Inc. has since shipped Releases 4 and 4.5 of HyperChem, is currently shipping a new Release 5 of HyperChem, and has delivered other new products such as ChemPlus, HyperNMR, and HyperChem Lite. The company is developing a range of new molecular modeling products for a range of platforms, although its dominant product remains HyperChem for Windows. A version of HyperChem for machines from Graphics, Inc., cancelled by Autodesk, is being delivered again.

The company's technical expertise involves both chemistry and computer science and an intimate mix of the two disciplines. Scientists at Hypercube are some of the best in their field and the company prides itself on its state-of-the-art approach to developing well-designed and engineered software that is both easy to use and appropriate to the molecular modeling needs of a broad spectrum of scientists.

The company intends to be a major player in chemistry software and a legitimate member of the community of scientists via products, publications, workshops, and other activities that serve to assist both researchers and educators in chemistry.

Hypercube, Inc. is now a focused, profitable, and growing molecular modeling company. Its products are primarily sold through a dealer channel, with dealers operating in over 30 countries.