Result Analysis Of Pymol Autodock Vina

Question

[Ritz]

I have done protein docking with some relevant ligands, now i am looking for the best molecules on the basis of highest docked energy and the interest of amino acid interactions? is this the right way to find the good molecule on the basis of docking or what more i can do in the result analysis? which one is more reliable compound for protein having highest docked energy or lowest ?

Answer 1

[Michael Schubert]

Docking scores are most often expressed as binding enthalpy. This means, the amount of energy that the system consumes to perform such a binding action is calculated. Now, as binding should should free energy rather than consume it you are looking for the most negative number (often kcal/mol or kJ/mol).

There are some things to consider besides the docking score itself:

• is the way your ligand is bound in the pocket by docking actually reasonable (no clashes, etc.)?
• did you generate enough poses so that it is oriented correctly (otherwise it would show a worse score than could actually be achieved)?
• do you have any biological data (e.g. a known inhibitor that you docked as well; as a general rule, it is always good to have controls) to support your conclusions?

[Ritz]

*well i dont have any biological data for molecule to support as i am doing in a very new target.

moreover i have generated 10 poses for each molecule but every pose shows different interactions and different scores, so for choosing one specific molecule out of 100s i am pretty confused.

we have some specific interest of amino acids and depending on that i am planning to suggest some molecule however those molecules different poses interacts differently..so will that molecule work for the target..what are the chances..is there something we can do with the poses?