Hi,
in order to visualize ligand - protein interactions in 2D view , i used MOE , ligplot+ and also visual discovery studio. but MOE and ligplot showed me few interactions ( they were almost H - bond ) Compared to discovery studio which showed me more interactions like van der waals , pi - anion , etc.
Now the question is why there is difference between them ? and which one shows more reliable and acceptable 2D interactions ?
Thanks!
It may because of different algorithm used for different software. I think Glide provides a more reliable and acceptable 2D interactions.
You might also want to try the Protein-Ligand Interaction Profiler PLIP
https://projects.biotec.tu-dresden.de/plip-web/plip/ ( https://academic.oup.com/nar/article/43/W1/W443/2467865 ) - it includes in its analysis some things most other s don't, e.g. water-mediated contacts, Pi-pi stacking, cation-pi interactions, metal mediated contacts.
As Annemarie Honegger said PLIP works well. Apart from PLIP I would also recommend you to try PyMOL (preset -> ligand sites -> cartoon) . It works quit well with protein-ligand complexes.
There is a user friendly 2D protein ligand interaction visualiser that can solve your problem but MOE is a commercial software
Actually, PLIP allows you to export the results as PyMOL session
The schrodinger maestro software is a very good tool
https://www.schrodinger.com/maestro
Dear Ali
You can use Discovery Studio visualizer software (version 16. 1. 0) . this software is free to download
To the second part of your question (why there is difference between them ? and which one shows more reliable and acceptable 2D interactions ?):
The energy function of any interaction is a continuous curve, and a somewhat arbitrary cut-off is chosen below which the interaction is no longer shown. In most programs, you can actually tweak the thresholds depending on whether you want to detect potential interactions with high sensitivity or whether you want to highlight only the strongest and most significant. For H-bonds, some programs entirely rely on the distance between donor and acceptor, while others also take into account the angle between donor, hydrogen and acceptor. Any set of coordinates is just a snapshot of your molecule. If you look at the interactions along a molecular dynamics trajectory, you will see the interactions blink in and out as the interatomic distances alter with the motions of the molecule.
In addition, many of the different interactions cataloged by the more discerning programs are just special cases of charge-charge and induced charge interactions, or the interactions of the orbitals as you go to a quantum chemical description of the molecule.
One of the things I like about PLIP is that it carefully explains what criteria it uses to detect the different interactions in its "HELP" file (https://projects.biotec.tu-dresden.de/plip-web/plip/help).
Is Schrodinger maestro free for use?
And anyone has any source for learning the software interface?
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