I have the following docking results:

Dock_1 has better energy score than Dock_2. What I want to do is to show with Pymol that Dock_1 is better visually.

Here I use hydrogen bond, highlighted with Yellow (Dock_1) and Gray (Dock_2). But as you can see, with that I can't show that Dock_1 is clearly better. That's why I'm looking for better alternative than hydrogen bond.

enter image description here


1 Answer 1


maybe you can use the "per-residue interaction scores" (wich is available via Schrödinger).

On the other hand,to show if a Docking Pose is really "better" you could show specific interactions rather than the complete big molecule.. e.g. an important salt bridge is missing. (hydrogen bonds are not that important, due to the fact that they can be bridged with water molecules)

Sorry, this is not really a solution, but I am not allowed to comment jet -.-

  • 3
    $\begingroup$ Totally. To further this, a salt bridge contributes something like -2.5 kcal/mol, while a h-bond -1 kcal/mol. pi-pi bond or S-pi about -1 kcal/mol, but that does not account for the improved solvatation term, which plays a role. Coordinated waters play a massive part in many protein, e.g. G-protein alpha–beta interaction, ribosome, barnase-barnstar etc., and a water can contribute some -3 kcal/mol. $\endgroup$ Jul 8, 2021 at 9:32
  • $\begingroup$ @MatteoFerla my key concern is to show that visually. Is there away I can show salt-bridge, pi-pi bond, S-pi bond with Pymol to show the difference of two docking? $\endgroup$
    – neversaint
    Jul 8, 2021 at 12:47
  • $\begingroup$ @Lucas thanks. Is there a way to show "per-residue interaction scores" visually in Pymol? Is there away we can systematically identify specific interactions that matters? Any reference on this? I appreciate your reply. $\endgroup$
    – neversaint
    Jul 8, 2021 at 12:54
  • $\begingroup$ @MatteoFerla Also, if I want to show salt-bridge with Pymol. What's the reasonable residue to choose from each ligand and receptor? $\endgroup$
    – neversaint
    Jul 8, 2021 at 13:05
  • 2
    $\begingroup$ Your E looks like a ∆∆G in kJ/mol, which means that they were docked with a forcefield method. You may have among the files a per-residue split of the forces. For PyMOL, select salty, ((byres (resn ASP+GLU around 3)) and resn LYS+ARG) or ((byres (resn LYS+ARG around 3)) and resn ASP+GLU) should work for salt bridges btween canonical amino acids. $\endgroup$ Jul 8, 2021 at 13:24

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