Computational Drug Discovery and Design

$ ../bin/RotaBond 3nw9_ligand.mol2

Then the output is printed on the screen (Shown in Fig.5).

The atom names forming rotatable bonds are listed in Bond records

(Bond 0 to 5). The last line shows the total number of rotatable

bonds.

3.5 AddH Program Usage:

AddH [input protein PDB file] [output PDB file]

The output PDB file include all the atoms in the input file as

well as added hydrogen atoms.

Example.

Open the terminal and change the directory to the installed

subdirectory of “example”. Run:

$ ../bin/AddH 3nw9.pdb 3nw9_protein_h.pdb

4 Case Studies

Molecular docking has been widely used in predicting protein–li-

gand binding conformation. It can provide information about the

binding mode, critical residues, binding affinities, etc. which are

very helpful to drug discovery and biological study. To evaluate

quality of docking prediction, docking result is often visualized by

3D visualization software to inspect the interface complementarity

manually. To aid the evaluation, protein–ligand scoring tools could

be very helpful. Here we provide a real case for evaluating the

docking result of a serine protease and dipeptide inhibitor by

using Cyscore.

The protein and ligand structure file (PDB ID: 1BMA, which

contains protein PDB file “1bma_protein.pdb” and ligand Mol2

file “1bma_ligand.mol2”) were down loaded from PDBbind. We

Fig. 5The output of RotaBond

Protein-Ligand Docking by Cyscore 239