I need to perform a covalent docking between a specific residue in my protein structure and glutaraldehyde as a ligand. I have tried few programs but I don't know how to identify my ligand as they use unspecific libraries and when I import the molecule myself the docking doesn't start running. I would like to know if anyone has any experience regarding this matter.
Normally you will need to in some way tell the program which are the reactive groups. You want to do covalent docking, not virtual screening, therefore you do not need a library of potential ligands, but need to prepare your specific ligand appropriately.
How to exactly do ligand preparation for covalent docking depends very much on the specific program you use,
e.g. https://www.youtube.com/watch?v=tS8xc5RcSQo for FITTED
https://www.youtube.com/watch?v=WwYYFnKmXls
https://www.youtube.com/watch?v=VtRzhsDzkv4 for ICM-Pro
https://www.youtube.com/watch?v=2CSiz5guoXg for SeeSAR
https://www.youtube.com/watch?v=PuyFhBkU8FM
https://www.youtube.com/watch?v=KcUUHkDgc7I for MOE
https://www.cresset-group.com/about/news/flare-v3-release/ for Flare V3
If the specific program you are using offers a tutorial with sample data, I strongly suggest that you first do the tutorial to be better able to discern at which step the procedure with your own ligand goes wrong:
e.g. for Autodock
https://autodock.scripps.edu/resources/covalent-docking/
Article Comparative Evaluation of Covalent Docking Tools
Article Covalent Docking in Drug Discovery: Scope and Limitations
Thank you professor Annemarie Honegger, I was confused because I couldn't figure out the issue with my ligand. I have watched the videos you recommended.
can pls specific with which software ur approaching and are u using windows, linux or mac.
Sethupathi Raj S I'm using SeeSAR which I find easy to deal with and I am running windows 10.
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