Step 6: Analysis of Docking results- Once the docking is over, apart from the free energy parameters, docked conformation of the ligand can be analyzed to understand the result.

Relevance of the docking result- There are multiple approaches to understand the relevance of docked conformation of a ligand molecule.

A. Docking against homologous host protein- A ligand molecule can be docked against a homologous protein from the host and the energy parameters can be calculated. A significant difference may give confidence that the ligand molecules will not bind to the host protein.

B. Comparison with the substrate molecule- To correlate the free energy value with the binding constant of the ligand, a comparison with the substrate molecule can be performed. A substrate molecule can be docked against target protein and the energy parameters can be calculated and used for the comparison purposes to in-directly understand the binding affinity of the ligand molecule.

5. In-silico toxicity prediction- The list of different softwares for toxicity prediction can be accessed at weblink http://www.click2drug.org/directory_ADMET.html . Most of the toxicity prediction software or web server either gives possibility of drawing the chemical structure or use the smiles of the ligand molecule to predict the toxicity in cell or animal based system. They also predict the carcinogenic and mutagenic potentials of the ligand in different systems such as cells, mouse, rat etc.