W56 Nucleic Acids Research, 2010, Vol. 38, Web Server issue Figure 2. ProteinDBS retrieval results visualization for global-to-global comparison. The top-left panel shows a superimposed view of a query protein chain and a selected result chain from the ranked list in the top-right panel (the third-ranked protein chain in this ﬁgure). 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 displays the structure alignment results represented by sequences with the RMSD and alignment length. For a global structure search, users can anticipate real-time results. Local structure searches, however, usually take minutes, dependent on the size of the query protein. Our system provides two options for the users: (i) the system will return a session ID for the query along with an estimated execution time after the query protein structure has been uploaded. The user can then bookmark the link of the session ID and check back with the result- ing page a few minutes later. (ii) If the user is willing to provide an email address when the query protein structure is uploaded, the system will send ranked results to the user’s email account.