I generated the complex of my protein and ligand and visualise it in Chimera and other visualisation software but I observed no interaction between my protein and ligand. What could be the cause of this?
Dear Larwubah Kollie
Did you've activated the complex interaction (P-L) in the software are you using.
If its still not working try with Maestro Free (Schrodinger LLC) to visualise the complex and hopefully your problems will be resolved.
Try to visualise it with any one of the following:
1) Discovery Studio Visualizer (https://discover.3ds.com/discovery-studio-visualizer-download)
2)PLIP Server (https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index)
3) Ligplot+ (https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html)
When you say interactions, have you seen the ligand atom distances from the protein. Have you used any modeling tool for designing the complex? Or was it docking?
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