Nucleic Acids Research, 2012, Vol. 40, Database issue D545 Figure 3. Result report of PoSSuM. Blue and green rows, respectively, show the known ligand-binding sites and putative sites. study (24)], aligned length and RMSD. In addition to protein names on the ninth column, CATH, SCOP, EC numbers and GO terms that users speciﬁed in the submis- sion form are shown. These structural and functional an- notations are useful for exploring similar binding sites from different folds or from different enzymes. Only a CATH and SCOP code that accounts for the largest part of the binding site is displayed if the binding site has multiple CATH or SCOP codes. The last column provides users with a powerful function to search similar binding pockets throughout the PDB rapidly. For example, if a known ligand-binding site of interest is detected using SearchP, then one might then be inspired to ﬁnd the binding sites that are related to the site. One could then simply click the ‘Search it!’ button at the last column instead of returning to the top page and resubmitting the site using SearchK. For further analyses, all results can also be downloaded as a plain text ﬁle, which includes a list of well-aligned amino acids whose interatomic distances of the Ca atoms are within 5.0 A˚ , as obtained from 3D superposition using TM align. Superposition on JmolApplet The ﬁrst column for each hit is linked to the superposition of the hit to the query site. The superposition can be visualized using the JmolApplet (http://www.jmol.org) on a web browser. To make JmolApplet available, the Java Runtime Environment (http://www.java.com/ja/ download/) should be installed on the web browser in advance. The query site and the bound ligand are shown as pink and red sticks, whereas the hit site and the bound ligand are shown as cyan and green sticks (Figure 4). For the putative sites, only the binding site is displayed with stick representation. Demonstration and application We next demonstrate the utility of PoSSuM database for ﬁnding ligand analogs that bind to similar protein regions