I am docking an intercalator (proflavine molecule) to DNA (PDB:1BNA) but I cant visualize their proper orientation. The ligand wont intercalate between the DNA bases. I need the details for GRID BOX like Grid BOX CENTER and Grid BOX SIZE. What parameters should I use?
I need help regarding the GRID BOX parameters. The ligand wont intercalate instead it acts like a groove binder.
Hi Nesteve, the DNA structure which you have selected for docking is not suitable. You have to take a DNA structure having preformed intercalation site(ex. 198D).
I have tried to use several overlapped grid boxes for docking and combine the result for further analysis.
I usually use receptor model already complexed with some inhibitor. This solves two major problems.
1. you do not have to bother where your ligand is going to bind (the problem you are facing now)
2. You can perform validation process by redocking the ligand back into the binding site and calculate RMSD. Validation is often demanded in many journals for publication.
It seems that model with PDBID 1BNA is not in complex with any ligand. If you are not compelled to use the same model for docking, I would advise you to change the model and use some DNA model that is already in complex with some inhibitor. PDB model PDB ID 226D shall be a good start since it is crystallized with inhibitor BIZELESIN-A
To specifically answer your question. I usually set The center of grid box on coordinates where experimental ligand is present. You can use default settings of Autodock for Grid box. Use the default parameters until you have very good reason to change the default parameters.
Hello Vikash Kumar and Rohan Meshram.
Regarding PDBID: 198D and 226D. Where should I position the grid box. What coordinates should I use for the grid box size and grid box center? X=?, y=?, z=?
Hi Xiaoquan Sun .
What should I do in order to use several overlapped grid boxes for docking?
In MGLTools , you can adjust the grid size. You can also move the grid to enclose the desired docking site. In your case try to enclose the intercalation site.
@Nesteve John Banghal. 4C55, no ligands inside, I need to find my own spots.
I work on a GRID managed from COMETA CONSORTIUM. It is a closed consortium open only to Cometa network members
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