Hi Maryam,

Have you validated the PDB ID you have chosen for the receptor? If not, first validate your PDB ID by calculating the RMSD of co-crystal ( in native state) and the pose after docking . If you are ending up with the same pose after docking, then your PDB ID can be a valid for your study. Kindly ignore this reply if you are already done with it. 

Thank you.

Thanks dear Naga.

I didnt neither validate the PDB ID nor I dont know how to do it, but I think it must work. Though, how can I validate it?

Hi Maryam,

I think Naga is right. You need to validate your docking parameters as well. If there is a co-crystallized ligand with your protein, you should remove it from the crystal structure then re-dock it. If you get the correct docking pose, then this should validate your protocol. Otherwise, tweak your docking parameters till you're able to reproduce the ligand's pose from the crystal structure.

Hi Maryam,

First: good points from Naga & Sara. Fist thing to do is to re-dock the ligand that was originally in the crystal structure and check that Autodock can retrieve the correct binding mode. If things go wrong, you can indeed tweak the docking parameters. But do not forget to check your ligand & receptor files as well. Common mistakes include bad ionization states (carboxylic acids, amines,...), bonds wrongly marked as non-rotable, bad geometries,... Such mistakes can obviously affect the quality of your docking.

Some notes on the RMSD values....

Happy docking

Sandro

Thank you so much for good information on RMSD.

I must think about the  parameters which  I can tweak...

any suggestions please?

Hello dear.

 i am suggesting you one article which will help to learn basics of docking.

doi:10.1016/j.ejps.2015.08.017

hope it will help you

thanks

All answers are valuable with your queries. For further assessment of docking results, you can employ DrugScore eXtended (DSX) server which further analyse the output from autodock. You can use PDB and SAR potentials for your work. 

What you need are: 

PDB file and posed ligand file (Which you will make after removing PDB from docked complex). You can use chimera for this purpose.

>Open the docked complex which you will select a best solution

>Remove PDB chain

>Save the ligand pose in mol2 format (you can also use .dlg file for this purpose)

>Open both files in DSX server, Use PDB and SAR potential

http://pc1664.pharmazie.uni-marburg.de/drugscore/

http://sw16.im.med.umich.edu/software/xtool/

Dear Maryam,

I also new at docking and i've once face those problem too. I think you could try to increase your number of GA runs to 100 and max number of evals to Long. Hope it will help.

Regards,

Mohammad Rizki Fadhil Pratama

dear mani... regarding to docking kindly ask this gentle man... named as mani maran, his mail id is [email protected]