The SiteAlign methodology projects topological and chemical properties onto a sphere that sits in the center of a protein pocket. The spheres are aligned based on these projections and a similarity score is calculated between the aligned fingerprints. Finding the right alignment is a time-consuming step, hence we offered SiteAlign already the KLIFS-aligned structures as a starting point and reduced the iterations as described in the KiSSim comparison to other methods section. KiSSim outperforms the SiteAlign results in most cases, however, often not considerably much.