How to validate a docking result?

maximos

Hi,

I use autodock vina for docking. My problem  is how to validate a docking results. I know that I should to compare with native ligand (co-crystallized ligand). but I don`t know how to do this and where is point?

Note : I performed the docking using the protein of sars-covid2 (PDB ID : 6LU7).

Many thanks in advance

Maximos

sobereva

If you already have crystal structure of ligand-protein complex, compare the structure difference after aligning the docked structure to the experimental structure.
If you do not have, you can perform molecular dynamics for the docked complex to check if it is stable and reasonable enough.

maximos

Thank you very much for the promt reply, and i don't have the crystal structure of ligand-protein complex, so i need to perform molecular dynamics for the docked complex, but i don't have much experience to handle Molecular dynamic, could you please advise me.

sobereva

You should use popular MD codes such as GROMACS, AMBER and NAMD to realize the simulation. MD is a key skill for studying ligand-protein interaction, you can find many materials from Google and official sites of the codes. (AMBER and NAMD have systematical tutorials on their websites)