Molecular docking
In a docking simulation, one or more small molecules (ligands) are fitted into an expected binding site on the surface of a protein target. The protein-ligand interaction is scored, and the best scoring binding mode is returned for each ligand, together with the score.
The steps to go through to explore protein-ligand interaction using docking, are described in the following:
- Setup the binding site in a Molecule Project (Setup Binding Site).
- Dock ligands imported to a Molecule Table (Ligand Docking Using the Dock Ligands Tool) or imported to the Molecule Project holding the binding site setup (Ligand Docking from the Project Tree Tool ).
- Inspect the docking results (Inspecting Docking Results).
Subsections
- Setup Binding Site
- Ligand docking using the Dock Ligands tool
- Ligand docking from the Project Tree
- The docking algorithms
- Inspecting docking results