Molecular docking guides

Guides on running and interpreting molecular docking with DiffDock and AutoDock Vina.

Superimposed protein folds with dotted connectors showing differences at corresponding positions.

Structures ·

What is RMSD, and what counts as a good value

RMSD is the average distance between matched atoms of two structures, in ångströms. Learn the formula, when to superimpose, and what values count as good for proteins, docked poses and molecular dynamics.

Small molecule in a protein pocket with dotted contacts and a magnified contact detail.

Docking ·

What is a Vina score, and what counts as good

The AutoDock Vina score is a docking score in kcal/mol, not a measured binding energy. Learn what the output columns mean, why there is no universal good score, and how far Vina tracks experimental affinity.