In July 1999, Quest Diagnostics, the nations leading provider of gene-based medical testing, information and services, and SBI announced a strategic alliance to jointly develop a series of database modules of novel, structurally variant proteins and market these products directly to the pharmaceutical and biotechnology industry for use in developing new therapeutic compounds. These databases are marketed under the Variome™ trademark. On December 14, 2000, Quest Diagnostics announced that it made an equity investment in SBI in connection with its ongoing relationship with SBI.

In November 2000, IBM announced that it made its first ever equity investment in a life sciences company: Structural Bioinformatics, Inc. It was further announced that IBM and SBI will collaborate to make the content of SBI's extensive database of protein structural information more readily accessible to researchers worldwide via the Internet on a subscription basis. Joint marketing efforts are planned. IBM is the world's largest information technology company, with 80 years of leadership in helping businesses innovate. IBM Life Sciences brings together IBM resources, from research and e-business expertise to data and storage management and high-performance computing.

In September 2001, SBI and ChemNavigator announced the signing of an agreement to combine SBI's proprietary technologies in three-dimensional computational proteomics with ChemNavigator's proprietary technologies in chemistry. The collaborative agreement will greatly facilitate the rapid identification of new drug candidates. Under the terms of the agreement, SBI and its customers can use ChemNavigator's 3-D database of two million drug-like compounds to screen in silico against the 2600 3-D proprietary protein structures in SBI's drug target database.