Autodock Vina Scoring Functions

[NeginManshour]

Hi,

I was wondering if I could use AutoDock Vina scoring functions to evaluate protein-peptide complexes.
I used Python-based scripts from the AutoDock Vina website just for scoring the complexes. A part of the script I used is as follows:

#Calculate box size (5 A larger than the ligand in each direction)
centers = []
max_width = 0
for array in [x,y,z]:
        max = np.max(array)
        center = (max + np.min(array))/2
        width = max - center
        centers.append(center)
        if width > max_width:
            max_width = width
box_width = (max_width + 5) * 2
box_size = [box_width, box_width, box_width]

for sf in ['vina', 'vinardo']:
    #Scoring using vina
    v = Vina(sf_name=sf)
    v.set_receptor(receptor_file)
    v.set_ligand_from_file(ligand_file)

    v.compute_vina_maps(center=centers, box_size=box_size)
    energy = v.score()

I obtained results using this approach. My question is: Is this the correct way to use AutoDock Vina to score these kinds of structures? Additionally, I understand that a more negative score (total value) indicates a better binding affinity. Is that correct?

Thank you for your assistance!

[rwxayheee]

Hi @NeginManshour
The script looks good. It prints exactly what I got when rescoring a Vina output

One thought: The box doesn't have to be a cubic box. You can compute the necessary length + buffering in each dimension and apply accordingly

[NeginManshour]

Hi and thank you for your response.

I just wanted to be sure that this scoring algorithm is also suitable for protein_peptide complexes. Since I got the results of this code. I just consider the "total" score as a reference for ranking. As I understand the less (more negative) score of "total" should be considered as a better score, is that correct?

[rwxayheee]

Hi @NeginManshour
Not entirely sure if it's suitable for protein-peptide complexes but the total score (1st element in energy) is indeed consistent with what used for ranking for poses of the same ligand. If the docking was performed from Vina you got multiple poses, and the best one has the most negative score.