Do It Yourself—Dock It Yourself: General Concepts and Practical Considerations for Beginners to Start Molecular Ligand–Target Docking Simulations

Medicinal chemists without practical molecular modeling experience are invited to practice simple docking simulations of small organic molecules into biomolecular targets. These targets are proteins such as enzymes, receptors, or ion channels in common cases, but can also be DNA or RNA or combinations thereof. Of note, the target is sometimes also referred to as macromolecule or biopolymer in the docking programs. In-house knowledge has been acquired over the last decade or so and is disclosed here to train users to practice docking on personal computers. This guide shows how to combine Autodock Vina with Autodock Tools, Swiss PDB Viewer, and Vega ZZ to prepare the input data and analyze the output data after docking. Special attention is drawn to include aspects, rarely laid open, about file management, input data preparation, and solving problems in a do-it-yourself manner. Pharmaceutical or medicinal chemistry knowledge is expected, while the practitioner is introduced step by step into the practical work of computational molecular docking simulations. The recommended way to use this chapter is to read through it first and then go into practical mode to carry out the docking simulation.