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

Figure 1

Superimposing of the complexed ATP (a), ADP (b), and AMP (c) structures. In (a), the Adenine structures of all ATPs are superimposed while the phosphorus atoms of the -phosphate (colored orange) are scattered in the space. In (b), the Adenine structures of all ADPs are superimposed while the phosphorus atoms of the -phosphate (colored orange) are clustered in a small range of the space. In (c), the Adenine structures of all AMPs are superimposed while the phosphorus atoms k2of the -phosphate (colored orange) are clustered in a small range of the space. It should be noted that the bond between phosphorus atoms is introduced by molecular visualization software and is not a real bond.

(a)

(b)

(c)