NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches

Figure 7

Comparison of the structures of templates identified by the NSiteMatch as similar to the chain A of the probable cell division inhibitor mind protein (PDB code: 1ION), which are classified as belonging to different superfamily as the 1ION protein. The 1ION structure is shown in red, while the three templates, phosphoenolpyruvate carboxykinase, UDP-N-Acetylmuramoylalanine-D-Glutamate ligase, and thermosome alpha subunit, are in green, blue, and grey, respectively. (a), (b), and (c) superimpose each of the templates to the 1ION structure by using Fr-TM-align. (d), (e), and (f) are the common substructures between the 1ION structure and a given template, which were identified by the NSiteMatch. The residues are displayed in the ball and stick format and the ADP is shown in the stick format.

(a)

(b)

(c)

(d)

(e)

(f)