ADL: Docking Entire Protein

James Lloyd James.Lloyd at nottingham.ac.uk
Sat Nov 21 06:06:27 PST 2020


Hi,

I am working with footprinting agents that covalently label the surface of a protein. By carrying out a differential binding experiment one can infer where ligand binding occurs.

I would like to simulate labelling of my protein with my footprinting agent and how this compares to experimental data. I have a python script which can run multiple vina docking events using a whole protein grid box, which then parses these runs into a single docking file. I am not so concerned about individual docking events but rather, the global docking statistics - i.e. where my label docks to.

I understand that AutoDock Vina was not created for such a purpose. Therefore I would appreciate some feedback as to the disadvantages/drawbacks I should be aware of when using Vina for this.

Thanks in advance,

James



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