Computational Drug Discovery and Design

warm color region in red circle is the active binding site of this

protein (Catechol-O-methyltransferase (COMT)).

3.4 RotaBond
Program

Usage:

RotaBond [input Mol2 file]

RotaBond outputs the number of rotatable bonds as well as the

list of atoms that form the bonds (seeNote 6).

Example:

Open the terminal and change the directory to the installed

subdirectory of “example”. Run:

Fig. 4The solvent accessible surface grid colored by surface curvature. (a) 3D visualization by Pymol. (b)3D
visualization by RasMol

Fig. 3The solvent accessible surface grid file

238 Yang Cao et al.