I am trying to calculate protein-ligand contacts (especially hydrophobic interactions) in the allosteric site of a GPCR. Thus, could you suggest a tool that I can use free of charge, except Desmond MD, to identify interactions such as H-bonds, hydrophobic, ionic, and salt bridges of binding site residues between a protein and a ligand throughout the simulation?
You can check Pycontact. Here is the tutorial.
-- https://pycontact.github.io/downloads/tutorial.pdf
You can always use VMD --> Extensions --> Analysis --> Hydrogen bonds or Salt bridges.
Since you mentioned allostery and GPCRs, the following git might be helpful for you.
-- https://github.com/barth-lab/AlloDy
Best,
Aysima
Try the Protein-Ligand Interaction Profiler (PLIP) https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
Aysima Hacisuleyman Many thanks for the information you have provided. After installing AlloDy with Ubuntu 2020.4 and Matlab R2023b, when I want to test the system using demo files, it always gives an error even though the database toolbox is installed. Later, after installing AlloDy with Macos m1 and Matlab R2021b, when I want to test the demo files, I still encounter the same database error. I haven't figured this out yet and I'm trying to figure it out but it seems very useful for determining the allosteric interactions of a GPCR.
Annemarie Honegger Thank you very much for your suggestion. PLIP is a useful webtool I have used before. I think I need to do more extensive interaction analysis to determine ligand interactions with a GPCR.
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