W220 Nucleic Acids Research, 2012, Vol. 40, Web Server issue and an ATP binding site in protein kinase C (PKC; 1xjd.A); the superimposition of these two binding sites is shown in Figure 4. Here, the ADP ligand of Ddl is superimposed upon the PKC inhibitor, staurosporine, as a consequence of the alignment of the two similar binding sites. This supports the suggestion that staurosporine may bind to Ddl, and that it should be experimentally tested for inhibition of Ddl. Off-target prediction Many inhibitors have been developed to compete for the ATP binding sites of protein kinases, but their poor se- lectivity usually eliminates them from consideration as clinical agents (34). The kinase 1z57.A is important in the control of alternative splicing and selective inhibitors targeting its ATP binding site have been developed. Debrohymenialdisine, for example, co-crystallized with human dual-speciﬁcity kinase, has been reported as 1z57.A (35), and we found that the ATP binding site of this protein kinase is similar to an ATP binding site in human ATP-citrate synthase (3mwd.A) as shown in Figure 5. Sequence identity of 1z57.A and 3mwd.A proteins is between 4 and 8% as computed by the FATCAT (36) and DaliLite (37) structural alignment algorithms. However, these two algorithms are not able to detect the binding site similarity. This result thus suggests that debrohymenialdisine, inhibiting the ATP binding site in this human dual-speciﬁcity protein kinase, would probably have undesirable side effects in human patients, due to off-target binding to ATP-citrate synthase. SOFTWARE REQUIREMENTS The ProBiS web server requires Sun Java plugin Version 6 Update 26 or higher (http://www.java.com), and has been shown to function correctly with Firefox, IE8, Chrome 14.0, Safari 5.1 and Opera 11.5 web browsers. It also works with OpenJDK (IcedTea-Web 1.1.1) plugin on Firefox. CONCLUSION ProBiS is a web server for detection of local structural similarities in proteins. It allows detection of similar three-dimensional patterns of residues in protein struc- tures irrespective of protein folds and with no prior know- ledge of binding sites. ProBiS enables the detection of similar binding sites in differently folded proteins, and can suggest protein targets amenable to drug reposition- ing. It can also be used to generate hypotheses for protein functions and for the prediction of off-target effects. To our knowledge, there is no such comprehensive, freely available web server that would allow these functions in this automated and intuitive manner. ProBiS can provide useful insights to experimentalists, and can directly suggest molecules that have a potential value in pharma- ceutical applications. 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