i want to do site specific virtual screening for a target. means i want to specify the residue in protein where ligand have to bind ..e.g i have a protein with 300 aa and i want to dock ligand at postion number 254. so is there any optoin in pyrx where i can screen ligand only for position number 254.thanks
In PyRx, that possibilities there. But some factor will determine these specific interaction like ligand donor, ligand acceptor, binding affinity etc. Sometimes
If you focus on specific residue, will not get the minimized binding energy. Based on your binding site residue (254) and ligand properties (molecular structure) will determine the interaction.
You can set the grid box center at "run vina" or "run grid" tabs (it depends wether you are using vina or autodock 4 within pyrx). You change it by manually moving the box on 3D scene window or by typing X, Y and Z coordinates (this option is available for newer versions only). For your purposes, you should set a grid box comprising the desired residues (like 254) and the software will find binding poses within that searching space, but it will not necessarily interact with all those residues as Selva Kumar said.
Rutash Kumar
I guess this PDF tutorial should help you the best https://faculty.missouri.edu/~gatesk/Docking_Assignment.pdf
thanks thirumal .i have one question if i select those position then it means ligand going to bind that positon .i tried this pdf tutorial but dont know binding is on desired position or not ...
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