Dear Research fraternity,
Is it possible to use multiple software tools for analyzing the same docked complex such as Maestro Visualizer, Discovery Studios, SEEsar, and UCSF Chimera to get consistent results?
In the case of amino acid interactions, I'm getting different results. Furthermore, the distance between residues varies as well when comparing the two visualizers for the same docked complexes.
With same viewing distance in each of the software, you should not expect different results. Possibly, the viewing distance in the two visualizers you are using are different.
@Rajesh Pal. Suppose we don't bother about the distance. But is it possible that the amino acid interactions are varied from software to software when we visualize the same complex in 2-3 softwares?
Banoth Karan Kumar No, the interactions can not vary. As Iqra Aroob mentioned, Only the way they are appearing can be different.
Most of the software on default settings may show different things. But, you can put the complex in PLIP, it should reveal all the interactions, irrespective of the distance.
Rajesh Pal Iqra Aroob I appreciate your clarifications.
I have attached an image of where the confusion began. Using Maestro visualizer for the first image and Discovery studio for the second.
In DS, I can clearly see some more interactions whereas this is not the case in Maestro.
Am I getting confused about how to interpret the results properly?
Banoth Karan Kumar Please read the manual for both the software carefully, especially the visualization sections.
Anyway, they look completely fine to me.
Maestro primarily displays H, H20, salt bridges etc with lines
Whereas, from DS legend it seems to me that Faded pink lines are some kind of hydrophobic interactions.
The Pi-Pi stacked bonds and the hydrogen bond are conserved in both of them.
Edit: bonds are similar in both, its just the software which displays them in different ways
I am facing the same issue while visualizing the docked result in pymol, DS, maestro, ligplot... all of them giving different results
Sneh lata Singh Yes, the same thing is till now sorted it.
If you find any answer to this, please let me know.
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