Hello, I am using CDOCKER of BIOVIA Discovery studios for Molecular Docking. I need to compare the binding affinity of small molecules to my protein target. I am doing a comparative analysis. My small molecule has a CDOCKER score of -3. I am trying to find better binding molecules than this molecule. I have my CDOCKER scores of positive (For ex.65, 79, etc) and negative values (For ex. -11,-35, etc). I need help in analyzing the binding based on scores. I have read that the high score value determines high binding affinity. Should I consider high positive value or high negative value as high binding affinity? what does the negative sign indicate? Need help on this.
Thank you in advance
In a nutshell, more negative binding affinity signifies better binding of the ligand to the protein, in other words, the corresponding protein-ligand complex is more stable compared to others. You should shortlist the ligands with greater negative binding affinities for further experiments/ investigations.
Visualize the structures of the two extremes -- it will be obvious which is better.
Both gentleman are correct, you also need to run a reference, a known affinity/standard compound!
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