In the query page for local-to-local search, users can perform various search options by specifying (i) the view mode of the results; (ii) the session ID that was assigned after the query was submitted; and (iii) a threshold for substructure sizes. The local comparison method supports three types of result browsing modes: M1, in which the top 10 SCOP folds with the best matched protein structure are shown; M2, in which the top 100 matched protein struc- tures from diﬀerent SCOP folds are displayed; and M3, in which the top 10 SCOP folds are presented with all matched proteins from the same fold. Figure 3 shows an example of M3, which organizes the retrieval results using a tree-view on the top-right panel. The top-left panel presents the superimposition of the query protein, 1o7j_A, and one of the top matched database proteins, 1gve_B, with a substructure size thresh- old of >3 residues. The common substructures are high- lighted with diﬀerent colors. The lower panel shows the sequence alignment result with RMSD and alignment length values. The users can use the ‘residue checkbox’ Nucleic Acids Research, 2010, Vol. 38, Web Server issue W57 and the ‘substructure bar’ under the residues to interact with the 3D superimposition view. The superimposition is shown with all the qualiﬁed substructures at the begin- ning. Each substructure pair is diﬀerentiated with diﬀerent colors in the 3D view and sequence alignment. When investigating a speciﬁc substructure, the users ﬁrst use the hyperlink ‘Clear Display’ to hide all the substructures and then click on the ‘substructure bar’ to show the sub- structures in the 3D view. Similarly, clicking on the ‘residue checkbox’ will highlight one designated residue. In addition, users can specify diﬀerent display themes, such as backbone, cartoon, strand and dots, by clicking on the corresponding label. All aligned protein structures can be downloaded from the result pages. Performance evaluation Two major performance evaluations have been conducted for ProteinDBS, namely retrieval accuracy and eﬃciency. If the top-ranked results are from the same structural Figure 3. ProteinDBS retrieval results visualization for local-to-local comparison. The top-left panel shows a superimposed view of a query protein and a selected result protein from the ranked list in the top-right panel (the ﬁrst-ranked protein chain in second-ranked SCOP fold). Users can check ‘Result Protein’ and/or ‘Query Protein’ to view the retrieved chain and/or the query chain. By clicking on a hyperlink below the top-left panel, users can view diﬀerent display themes. The lower panel shows the sequence alignment. Clicking on ‘residue checkbox’ below a pair of residue will highlight residues in the 3D superimposition view. To show one speciﬁc substructure, users ﬁrst click hyperlink ‘Clear Display’ to hide all the substructures and then click substructure bar to show the designed substructure.