Docking the ligand

There are many approaches to molecular docking and the subject has recently been reviewed [53, 54], Automated docking can be used to explore the 

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Dock the ligand using the default partial charges taken from the docking MM forcefield. 

Dock the ligand again, this time using the optimised partial charges. 

Fig. 9. Unlike the traditional ensemble docking, the 4D protocol docks the ligand into a set of receptor conformations in a single docking run.

Some of the methods described above automatically dock the ligand into the active site model. Several of the programs will also provide a numerical estimate of the goodness of fit, which is used as an indication of potential activity. 

In the cross-docking studies, we docked the ligand from one complex into the receptor of the other complex and vice versa. The RMSD values between the predicted poses and the experimental data are reported in Fig. 1 and are color mapped as described before for the re-docking. 

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