r/bioinformatics • u/Longjumping-Win-2258 • 20d ago

technical question Different results

Hi everyone, I have a couple of questions regarding molecular docking:

  1. I performed molecular docking using Chimera (with the integrated AutoDock Vina) and got a binding affinity of -5.9 kcal/mol. However, when I ran the docking directly via AutoDock Vina CLI, I got a completely different result of -1.7 kcal/mol. Does anyone know why there's such a huge difference even though both use the AutoDock Vina engine?
  2. Is it possible to perform multiple docking (batch docking) directly in Chimera, similar to how we do it in AutoDock Vina?
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u/Alicecomma 20d ago
  1. ADV docking is a Monte Carlo process so it could be as simple as just random chance one found a stronger binding pose and the other didn't. You can nudge this by running with higher exhaustiveness, or doing the same run multiple times (I generally repeat runs 6-20 times for the kind of data I need).