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

Figure 6

Binding sites predicted by the NSiteMatch, Findsite, MetaPocket, and Q-SiteFinder for chain A of the MJ1225 protein (a) and chain A of the cell division inhibitor mind protein (b). The predictions by NSiteMatch, Findsite, MetaPocket, and Q-SiteFinder are denoted with green, red, purple, and blue spheres, respectively. The ligands are in the stick format and are colored in black. The MJ1225 contains 3 ADP-binding sites and 1 AMP-binding site and the top 4 predictions from each method are shown. The cell division inhibitor mind protein has 1 ADP-binding site and the top prediction for each method is shown.

(a)

(b)