How to chose best ligand option based on affinity and RMSD from Autodock vina docking results?

Question

[maria2019]

Hi

I have docked 20 ligands to a protein using Autodock vina (with 10 poses for each ligand).

Now I want to choose the "best" mode for each ligand and then best ligands (based on the selection of 1). I Know that just these numbers will not be accurate and I will have to look at the 3D as well.

My questions:

1. I know that the first thing to consider is the lowest binding energy BUT the first one is always comapred to self. Does it mean that I should chose the 2nd?

2. Then, which RMSD I should chose? (upper or lower?)

for example, I have the following result for 1 ligand, What is the report that I should chose from the example for affinity and RMSD? (-9.0 and 2.27??)

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1         -9.2      0.000      0.000
   2         -9.0      2.275      3.262
   3         -8.9      2.759      7.245
   4         -8.8      2.113      4.472
   5         -8.5      4.396      8.519
   6         -8.5      2.421      4.606
   7         -8.5     24.699     27.660
   8         -8.5     22.339     25.282
   9         -8.3     16.071     19.273

Answer 1

[lucaspalmeira.1945]

I think it is okay to choose the first pose taking into account the RMSD. You can analyze which pose performs the most interactions and hydrogen bonds with the amino acids in the active site. Remembering that poses like the seventh, eighth or ninth position are not so recommended to use. Read the AutoDocking Vina article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/