I have solution NMR structure of a Nucleic acid that I have retrieved from PDB and a small molecule in SDF format from PubChem db. I need to figure the binding affinity of the small molecule with the Nucleic acid. Since the crystal structure is unavailable therefore I am left with the solution NMR structure file. So is there any different approach for docking solution NMR structures or I should follow the same approach used of crystallographic structures. And will the docking algorithms generate significant results if i follow the traditional approach of crystal Structures files?
You can build a 3D structure using homology modeling and then you have to compare your NMR structure with modeled structure after that, you can do the molecular docking. To know the binding stability of your small molecule within the binding cavity of receptor you have to perform MD simulation. If you have any further queries you can directly contact me (Email ID: [email protected]).
This work gives a detailed explanation about your concern: Journal of chemical information and modeling, 2009 49(8), 1925-1935.
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