I am docking multiple ligands (new designed ligand) against my protein using Autodock Vina in Chimera. The results displayed in this program are somewhat strange, because in some cases the ligands with no hydrogen bond or fewer bonds has the most negative Score than the ligand with more hydrogen bonds!!? Please look at the picture to get my mean(The best model in ligand with 2 hydrogen bonds has a score -8.3, While the best model in ligand with one or zero hydrogen bond has score -8.7 and -10.1 respectively!).

I understand that checking with other software or tools like PyMOL or PDBSUM will better help to analyze the possible interactions, however since I have several ligands with almost similar score and interaction network or equal hydrogen bond numbers, I am curious to now how to pick the best one (based on the in silico analysis) among them. If any body has suggestion for this I will appreciated it.

Similar questions and discussions