I have done a docking study by using mcule.inc web-service. I got the .pdb file of my protein-ligand complex from there. As I am using a free student account, I don't have access to more advanced functions. Is there any way to get the binding energy of that protein-ligand complex? I also need to know the type of interactions involved and their details in that complex. Is there any way to get that information from the .pdb file?
Hi Animesh Roy ,
I am not familiar with mcule.inc web-service but you can use the generated pdb file in several free software/tools to further analyse the interactions.
Here are some of the free software that you can use and there are plenty of tutorials and youtube videos on how to use them:
- UCSF Chimera: https://www.cgl.ucsf.edu/chimera/download.html
- LigPlot or LigPlus: https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html
- BIOVIA Discovery Studio Visualizer: https://discover.3ds.com/discovery-studio-visualizer-download
All the best and hope this helps.
Hi Animesh Roy ,
- A quick way to find out the binding energy/affinity of your docked complex is via the PRODIGY webserver (https://wenmr.science.uu.nl/prodigy/).
- To analyze/plot protein-ligand interactions, there are several options as listed in the answer above but yet another option would be the PoseView program via the ProteinsPlus webserver (https://proteins.plus/).
Best regards,
Ajay
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