Nursing

Gene

Virtual screening

Biology

Visualization

AutoDock

Receptor

Biochemistry

Data mining

Computer science

Docking (animal)

Computational biology

Drug discovery

Ligand (biochemistry)

Protein–ligand docking

Medicine

Chemistry

In silico

Journal of Computer-Aided Molecular Design

Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and interactions are mandatory. Here we present an interface between the popular molecular graphics system PyMOL and the molecular docking suites Autodock and Vina and demonstrate how the combination of docking and visualization can aid structure-based drug design efforts.

Ligand docking and binding site analysis with PyMOL and Autodock/Vina