The Molecular Graphics Laboratory Forum

Dear everyone,

I am getting stuck in analyzing the results. I don't know after docking in Autodock Vina, whether do we need to superimpose the structure of protein before and after docking or not. And if yes, which the structure is the structure of of protein after docking?

Could you help me to answer these questions?

Many thanks for your help and your time.

I use pymol to view vina results. open ligand conformations, then open the same protein pdb or pdbqt u docked upon earlier. if your binding site was correctly input then ligand will be snugly fit there. if the ligand u r docking and protein have a prior crystallographic data in pdb format, then u can remove that ligand and dock that same ligand in that same receptor to see how compatible your docking is too the real thing. The more compatible in shape , the more arguable docking results will be. This step is like a type of quality control of your docking. The idea is that ligands with more free energy make tighter fit and a tighter fit is a prerequisite for activity. But higher free energy does not need to translate to better biological activity. So a check of conformational superimposition with existing drug receptor conformation is our best shot at mimicking natural binding poses.

Thanks so much for your reply.

I only got -4.8 binding affinity in vina with those tutorials but the video tuturial shows -16 binding energy. how much did u get on the tutorial? pls send me your config and log files.

Hi,Sagarriya,

I am so sorry because I don't understand what you mentioned. Can you tell again for me to send you files if I did it?

Cheers,

Hello,
I am also getting -4.8
Is that bad? Does it mean I am doing something wrong? Thank you, the people here are so helpful.

It seems so that we did something wrong. the -4.8 is a measure of how readily drug receptor complex forms. The more negative the better.
The real point is how come tutorial does same thing as us and we get different result. We should also have -16.

Also someone pls post scripts for metal enzyme docking. I can't find it anywhere