I used AutoDock Vina to dock a drug with a protein. this gave me a list of conformations with the different binding affinities. I selected the more negative one to analyze it using PLIP webserver which gave me the different bond types between the drug and protein (H-bonds, hydrophobic, salt bridge, etc..).
My question is:
Is there a reference that describes the effect of each bond on the binding or how important each bond is for the binding?
thanks
Hi,
This thread might be helpful. https://www.researchgate.net/post/Which_interactions_are_more_significant_in_molecular_docking_Covalent_or_non-covalent
There are only two types of nonbonded interactions: electrostatic and nonelectrostatic; hydrogen bonds and salt bridges belong to the former. The importance of each electrostatic interaction depends on its strength, which depends on the partial atomic charges and on the distances between them (Coulomb's law).
Hi,
You would need to employ more robust methods (end point binding free energy methods) to quantify the importance of polar and non-polar contributions in the affinity.
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