W556 Nucleic Acids Research, 2009, Vol. 37, Web Server issue Figure 1. An example of using seeMotif by combining two motifs from diﬀerent computational tools. This ﬁgure comprises ﬁve parts: (1) motifs; (2) position mappings between the motifs and the reference sequence; (3) reference sequence with the matched positions highlighted; (4) a snapshot of the structure panel; and (5) local alignment of the reference sequence and the selected protein chain. In this example, motifs are plotted on the PDB structure 3PRK:E. Protein chains are shown in strands style. The residues matched by any of the motifs are illustrated as sticks with distinct colors corresponding to their sequence expression form in the sequence panel. Ligands (the inhibitor in this structure) are displayed in spaceﬁll and colored in CPK mode. Figure 2. An example of using seeMotif by combining ﬁve motifs from both computational tools and existing motif databases. This ﬁgure comprises ﬁve parts: (1) motifs; (2) position mappings between the motifs and the reference sequence; (3) reference sequence with matched positions highlighted; (4) a snapshot of the structure panel; and (5) the motif selection panel in the intermediate page. In this example, motifs are plotted on the PDB structure 1SCJ. Protein chains are shown in strands style, where each chain has its own color. The residues matched by any of the motifs are illustrated as sticks with distinct colors corresponding to their sequence expression form in the sequence panel. CA ions are displayed in spaceﬁll. in binding other molecules, it is suggested to sort the struc- tures by the nearest distance between any matched posi- tions to any ligands or small ions found in the structures. Another way to explore the structures is sorting them by the total number of positions matched by the motifs (#MR as the column name). Finally, structures can also be sorted according to the proportion of surface residues among the set of matched residues (%Sur). How the motifs interact with each other in space can be viewed in the structure panel. Furthermore, it is shown in