Nucleic Acids Research, 2012, Vol. 40, Web Server issue W219 Figure 5. Superimposition of similar binding sites in dual-speciﬁcity kinase (1z57.A; blue) and ATP-citrate synthase (3mwd.A; violet). The superimposed residues are thin wireframe models. The inhibitor debrohymenialdisine is colored blue and is a thick wireframe model. or PDB ﬁles; and (v) searching within the table of similar proteins. A complete list of new features is available in the User’s Guide at http://probis.cmm.ki.si. ProBiS web services RESTful web services have been implemented to allow access to the ProBiS web server by user written programs or scripts. A list of commands available is on the ProBiS web server home page. Methodological improvements Statistically meaningful ranking of the identiﬁed locally similar proteins or binding sites is achieved through the use of standard scores (Z-Scores) (27), which replace the various alignment scores described previously (26). EXAMPLES Binding sites detection For the query protein (PDB/Chain ID: 2q4u.A), ProBiS accurately detects three conserved binding sites as shown in Figure 3A. The Ca2+ ion, which is co-crystallized in the similar protein calcineurin B (2ehb.A), is shown in Figure 3C, and reveals a probable binding pose of the Ca2+ in the query protein. Proteins 2q4u.A and 2ehb.A have similar binding sites, despite their low amino acid identity, i.e. between 2 and 10%, as judged by different pair-wise structural alignment methods in the ‘3D Similarity tab’ at the RCSB PDB Web page (28). ProBiS also predicts binding of 5 other Ca2+ ions to the query protein, which is not shown in Figure 3; these can be seen by viewing alignments 1–4 in Jmol for the similar protein calmodulin (1fw4.A). Drug repositioning ProBiS can detect weak binding site similarities in proteins with different protein folds. Here, we present an example of drug repositioning. Protein kinase inhibitors were con- sidered for inhibition of bacterial enzyme D-alanine– D-alanine ligase (Ddl), based on the similarities between ATP binding sites in protein kinases and in Ddl (32,33). However, repositioning was only done for a small propor- tion of all available protein kinases, which manifested this similarity. Using the ATP binding site of Ddl, 1iov.A, shown in Figure 2, as the query, ProBiS detects a previ- ously unrecognized similarity between this binding site