W216 Nucleic Acids Research, 2012, Vol. 40, Web Server issue proteins, and provide increased annotation of uncharac- terized protein structures, drug repositioning and off-target predictions. Details regarding the new ProBiS are available at http://probis.cmm.ki.si. ProBiS WEB SERVER Input An example of the input to ProBiS is shown in Figure 2. The user ﬁrst deﬁnes the query protein by either providing PDB/Chain ID(s) or uploading a PDB ﬁle. In the ﬁrst case, a yellow pop-up window appears, containing a link to the ‘Local Structural Similarity’ web page with the pre-calculated results for a homologous member of the nr-PDB. Following this link, the results are taken directly from the ProBiS-Database, and no computations will be performed; in the other case, one continues with de novo search for structural similarities. This can option- ally be limited to a speciﬁc region on the query protein surface, for example, a binding site, by clicking the ‘Select Motif’ button, shown in Figure 2. This opens a new browser window with the 3D query protein model. A binding site, or any other part of the protein, can then be selected by clicking on the query protein 3D model; the surface atoms within a radius of 15 A˚ around this selected point are highlighted in yellow. This default value of 15 A˚ can be changed in the text box above the ‘Select & Close Window’ button. When the window is closed, the selected, highlighted surface is converted to a text format in the ‘Residue Motif’ text box, and can be immediately used as the input to the ProBiS web server. This enables selection of binding sites to be used as queries. The comparison database can also be changed in the new ProBiS web server and the query can now be compared against either the non-redundant PDB (default) or a custom list of any protein structures. The latter are represented by the PDB/Chain IDs, e.g. 1all.A, 3dbj.C, 2vjt.A, which can be entered into the text box that opens when the user selects the ‘List of PDB/Chain IDs’ option in the ‘Comparison Database’ drop-down list. Access to the pre-calculated similarity proﬁles in the ‘ProBiS-Database’ is provided through the search text box located on the top of the ProBiS web server page as shown in Figure 2, and through ProBiS-Database widget or ProBiS-Database web services, which have been described previously (27). Output The ProBiS output page shown in Figure 3 contains the query protein cartoon model 2q4u.A colored according to degrees of structural conservation from unconserved (blue) to structurally conserved (red) and visualized in an integrated Jmol molecular viewer (see panel A). The structurally conserved residues are shown as red spheres and indicate the location of the putative binding sites. There is also an interactive table of available similar proteins (see panel B). Clicking on the ‘View’ link in the ‘Alignments’ column shows the superimposition of the query (2q4u.A) and the similar protein (2ehb.A), and opens the ‘Details’ tab of residue–residue correspondences of all alignments between the query and the similar database protein as shown in panels C and D. Clicking on any protein chain link in the ‘Chain’ column opens a new output page with the pre-calculated structural simi- larity proﬁle for a homologous member of the nr-PDB. The ‘Name’ column presents the names of the similar proteins; the ‘Pfam’, ‘SCOP’ and ‘UniProt’ columns provide links, where available (31), to the corresponding external protein annotation resources. The similar Figure 2. Detection of Structurally Similar Binding Sites. ProBiS input page. Detailed instructions are provided in the User’s Guide at http://probis. cmm.ki.si.