As I am new to docking part, wanted to know that is a more negative docking score in RMSD table is better or positive score is better.
As i have read two recent papers in which both are explaining different information related to docking.
I want the clarity in the docking score which better for research purpose?
The RMSD (root mean square deviation) would be a positive number. It is a measure of how close a given structure is to a reference structure, so that the closer the RMSD is to zero, the better.
In contrast, some docking algorithms compute a docking score that is related to the free energy of binding of a ligand to a receptor. For this type of docking score, the more negative the score, the better.
Docking scores are good if they are in (semi)quantitative agreement with binding free energies.
Quantitatively, docking scores with more negative binding energy values are considered good i.e. -6.01 is better than -5.9
Negative binding energy is better than positive binding energy.the more negativity of the binding the stronger / stabler the protein ligand complex.
As a structural biologist, we recommend you to never believe the docking score or binding energy blindly. Some times the binding pose may be at the right site with relatively high energy than the reference structure. One way to do this is to compare with the existing PDBs.
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