Like many bioinformatics companies, Inpharmatica uses public domain databases to draw comparisons with clients' proprietary sequences. However, instead of simply comparing unknown client sequences with annotated public sequences to predict functionality, Inpharmatica also compares 3-D structure with 3-D structure. This can group proteins by their structure and allows the detection of genes with different sequences but potentially the same function.

The company's approach is based on the variety of skills brought to it by its five founders, which the company says gives Inpharmatica the ability to view bioinformatics in new way. Janet Thornton is a pioneer in bioinformatics and has been developing biological databases over the last 15 years. David Jones brings expertise in protein structures and sequences. Teresa Attwood has knowledge in attaching annotation to database information, Christine Orengo works in protein classification, and