10
$\begingroup$

I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein.

There is a particular target for which AMDock Vina, with its default force fields, predicts that certain molecules will dock very well. But the follow-up experiments do not show any activity.

I have read a comment that it is possible to use experimental data to customise the force field in AMDock Vina. I would like to use the data from the experiments to customise the force fields that Vina is using. But I cannot find any good documentation on the subject.

Can anyone please point me to some resources?

$\endgroup$
8
$\begingroup$

Changing the force field parameters is not a good/recommended approach. This is due to the high number of parameters you have to know. Many of them, you cannot obtain from experimental data. Instead, you will need high precision methods like Density Functional Theory, Hartree-Fock, pos Hartree-Fock or semi-empirical methods to calculate them for two, three and four atoms sets.

One thing that affects more the quality of the results is the score function used by the docking software instead the fore field.

My recommendations are two:

  1. Move to another docking software, like PLANTS, GOLD, GLIDE, etc.
  2. Do the docking with the program you want and them do a re-score in place using a better scoring function like ChemPLP (from PLANTS), X-SCORE (empirical scoring function) or DLSCORE (deep learning based).
$\endgroup$
1
  • $\begingroup$ Thank you very much for that advice. I will try to find information on point 2, especially on how to use an empirical scoring function. I see something about it in the AMDock documentation, so I hope that will be sufficient. $\endgroup$ Jun 10 at 6:35

This site is temporarily in read only mode and not accepting new answers.

Not the answer you're looking for? Browse other questions tagged .