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

Table 3

The templates identified by NSiteMatch for the probable cell division inhibitor mind protein. Three templates, namely, phosphoenolpyruvate carboxykinase, UDP-N-Acetylmuramoylalanine-D-Glutamate Ligase, and thermosome alpha subunit, have different topologies but similar binding segments and binding sites to the predicted protein.

Polymer name	PDB code:(chain)	Binding segment							SCOP label
Cell division inhibitor mind protein	1ION:A	G	T	—	G	K	T	T	c.37.1.10
Phosphoenolpyruvate carboxykinase	1K3C:A	G	T	—	G	K	T	T	c.91.1.1
UDP-N-Acetylmuramoylalanine-D-Glutamate ligase	2JFG:A	G	S	N	G	K	S	T	c.72.2.1
Thermosome alpha subunit	1Q3S:A	G	D	—	G	T	T	T	a.129.1.2