Docking
A ligand docking simulation sample how the ligand can fit into the binding site specified by the Binding Site Setup. When the simulation has ended, the best scoring binding mode will be returned as a result, together with the score (Molecular docking).
It is always a good idea to check that experimental knowledge about protein-ligand binding can be reproduced or supported, by docking a known ligand into the binding site setup.
Examples of experimental knowledge:
- Ligand binding mode known from crystal structure
- Binding mode of a very similar ligand is known from crystal structure
- Some information about protein-ligand interaction is known, such as which amino acids are interacting with the ligand
To improve the docking accuracy, a number of points can be considered relating to the protein target (Protein Target), the ligand (Ligand) and the docking simulation (Docking simulation) itself.