Example of the interactive plugins developed for UCSF Chimera using the serine protease example from Figure 1. A) Each hit is displayed in a pull down menu with the associated Z-score. When selected from the menu, the structure is downloaded from our web service and displayed alongside the query. A text box in the plug in window displays all matched environments between the query and the hit and the associated Z-score. When those environments are individually selected, the query and the hit are superimposed using the Chimera match command based on the backbone atoms of the matched residues. A ClustalW based alignment is available by clicking the appropriate button. B) The common functional annotations of the hits are used to annotate the query structure by determining how closely associated each environment is to a given annotation. The most closely associated residues are highlighted in darker shades of green, and different thresholds can be selected.