Autodock Vina Results: Binding Affinity (Kcal/mol) - (Jul/09/2013 )
First of all, I am very new in molecular docking field.
I am using Autodock Vina with PyRx Virtual Screening Tool.
For the part for "analysis results", there are: Binding Affinity (kcal/mol); mode; RMSD lower bound and RMSD higher Bound.
The question is:
1) if I were to analyse my docking results, how does Binding Affinity relates to RMSD?
2) I understand that the lower the binding affinity, the stronger the ligand bind to the protein. However, is there any energy values that we can consider it "significant" or strong? For example, is binding energy -2.0 is strong enough, or it must be -8.0 or -5.0 and above? This is because I do not find it in any of the manual.
Thank you for your help in advanced.
More the negative value more better indicator it is. below -1 it should be ok. u have to select most Negative one.
note.- I asked my friend about it, he told me so. I used autodock once or twice only, if I will know more I will let u know.