I have a diterpene compound which showed significant anti-HIV activity and my supervisor had it docked and now I have a paper of results which some factors have been mentioned and unfortunately I don't know how to write a report of them for our manuscript. It should be added I can send you results.
1.see H-bonding interaction
2.Pi-Pi interaction
3.bonding with PAS amino acids
4.which part of your ligand fit into hydrophobic bonding pocket.
Describe the docking parameter used for this ligand-protein docking. describe scoring functions (Binding Energy (kcal/mol), Ki (µM), Intermolecular Energy (kcal/mol) vdW + Hbond + desolv Energy (kcal/mol), Electrostatic Energy (kcal/mol), Final Total Internal Energy (kcal/mol), Torsional Free Energy (kcal/mol), Unbound System's Energy (kcal/mol), Temperature(K). characterize the binding mode of ligand and protein in reference to binding pocket of your protein.
Read a couple of papers that describe ligand docking and observe how results have been reported/analyzed. It would be beneficial to compare docking results of analogues of your molecule of interest, if available.
I see many docking papers without proper controls (I am from wet lab where we always worry about proper experimental controls !). For e.g. the grid on the target must be defined and fixed, especially when different ligands are docked to 1 target...but this is not stated clearly. If one has an interesting ligand, one should dock it to the functionally active site of the desired target and to far away sites..this will tell us how specific and biologically significant the binding is. This is easy for enzymes..because active site is well defined..but not so easy with receptors. There are many pdBs for a given target..so if one gets an interesting dock, one should be able to demonstrate it with another pdB for the same protein target. Hope this helps!
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