Nucleic Acids Research, 2010, Vol. 38, Web Server issue W55 Figure 1. ProteinDBS v2.0 system architecture which has ﬁve modules (i) query interface; (ii) protein structure data management; (iii) data pre-processing; (iv) search engines; and (v) retrieval result visualization. structures is returned to the user, eight at a time. To visualize the quality of the search results, a 3D superim- position of the query and the top-retrieval result are displayed to the user. The user can select any of the ranked results from the top-right panel. Figure 2 presents a new interface for the superimposition view of the query protein chain and the top-ranked result, 1jsr_B, which is generated by clicking on the thumb- nail image on the top-right panel. The sequence align- ment result is also displayed to the user with root mean square deviation (RMSD) and alignment length values.