Constructing a set of sequence profiles to represent a conserved structural feature. Caspase's active site is highly conserved (1ICE, conservation levels are calculated using the von-Neumann entropy and displayed in a color gradient from blue (variable) to red (conserved)). Conserved residues in close vicinity of the tetrapeptide inhibitor largely define the catalytic site environment. Caspase residues within 5 Å of the inhibitor are underlined. Segments are patched and those with low conservation are discarded to avoid insignificant hits. We add the amino acid distribution from HSSP data for each site of the remaining segments. It is thus possible to construct HMMs and visualize the profiles as sequence logos .