Figure 2 that seeMotif can show the motifs on more than one chain in the same PDB structure. This facility is par- ticularly useful when studying quaternary structures and can be easily extended to exploring protein–protein interactions. In the last example, we demonstrate how to use the option structure selection through interaction network. In this example, the SV40 large T antigen (UniProt ID: P03070) is used as the reference sequence. With the refer- ence sequence, seeMotif identiﬁes its binding partner (P06400) and ﬁnds two complex structures (1GH6 and 1GUX) containing P06400. After that, the motif ‘L.C.E’ is used to scan the binding partners of P06400 in these two structures and successfully found two protein chains (1GH6:A and 1GUX:E) to visualize the motif. CONCLUSION AND FUTURE PERSPECTIVES In this article, we present the seeMotif server that aims to visualize sequence motifs on 3D structures related to a given reference protein. seeMotif provides an easy-to-use interface for submitting motifs in diﬀerent formats. Visualizing the spatial characteristics of motifs in an inter- active way and exploring the relationships between motifs in diﬀerent structures largely help to understand how a cluster of particular residues aﬀects protein functions. seeMotif will be regularly updated based on the newest release of UniProt, PROSITE, ELM and PDB databases. Furthermore, how to exploit seeMotif in detecting protein–protein and protein–DNA interactions deserves further studies in the future. FUNDING National Science Council of Republic of China, Taiwan [NSC 96-2320-B-006-027-MY2, NSC 96-2221-E-006-232- MY2, 97-2627-P-001-002 and 97-2221-E-002-184]. Fund- ing for open access charge: National Science Council of Republic of China, Taiwan. 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