Example of binding site comparison. Comparison of the binding sites of two cyclooxygenase (COX) enzymes was carried out using SiteComp. COXs are targets for non-steroidal anti-inflammatory drugs. (a) SiteComp difference region (white surface) favorable for COX-2 (gray sidechains) over COX-1 (black sidechains). (b) The non-selective COX inhibitor Ibuprofen (gray) does not take advantage of the difference region, while whereas the selective COX-2 inhibitor Celecoxib (black) occupies most of the predicted selectivity region (Wang, et al., 2010).

Example of multi-probe characterization. Sub-sites in the active site of adenylate kinase (ADK) were identified using SiteComp. ADK catalyzes the phosphate transfer from ATP to AMP. The figure shows AP₅A, an ADK inhibitor (Abele and Schulz, 1995) that mimics the structure of the two substrates in the ADK active site. Sub-sites identified with the methyl carbon probe (white surfaces) highlight the regions of the active site that recognize the adenosine groups in the inhibitor and the substrates (thin lines), while sub-sites identified with the phosphate oxygen probe (gray surface) delineate the phosphate transfer region (thick lines).