Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?

Question

[srdjanmasirevic2]

Hello,

I have use DOCK to dock 10 ligands into the protein structure.

I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in one pdb file.

Now, what I want to know is when I give this file to LIGPLOT, is it possible to generate something like:

%polar interactions XX
%non-polar interactions XX
%hydrogen interactions XX

Is there a way to do it with LIGPLOT, if now is there some other software that can be recommended for this type of assessment?

Best

Answer 1

[Mensur Dlakic]

I have given an example of the LigPlot+ output here. It doesn't show percent of bonds, but it makes a nice visual.

As to showing an ensemble of multiple ligand conformations along with the receptor, it is simply a matter of getting all the ligand coordinates into the same PDB file and giving them unique chain letters. This one has 17 different ligand conformations.

[srdjanmasirevic2]

Thank you Professor Dlakic very much!

Is it possible to visualize or get a number of electrostatic on the one side and Van der Waals interactions on the other side?

I am accessing different binding modes of several ligands docked in two structures (1 and 2) of the same protein and since I get better docking scores (or enrichment) for structure 1, I wanted just to see if structure 1 has more polar/nonpolar/hydrogen interactions then structure 2. Or in other words, why structure 1 if it is a same protein manages to give me better "score" or enrichment for my 10 database ligands. I think it has something to do with from the interaction point of view as other, more general things such as Volume, SASA I have excluded already.

Best, Srdjan

[Mensur Dlakic]

As you know, it is difficult to identify correct binding modes by score alone. That's the whole point of clustering multiple solutions. Assuming that you have done flexible docking in both cases as recommended for small ligands, the explanation for the binding difference may be in initial differences in structures. Either way, LigPlot+ can do side-by-side (or overlaid) comparisons when "two or more ligand-protein complexes are sufficiently similar."