Molecular Docking with AutoDock VINA and PyRx

Overview

Teaching: 30 min
Exercises: 180 min

Questions

• How is molecular docking used to screen for small molecule binding?

Objectives

• Students will explain the file types used in PyRx.

• Students will use appropriate inputs and outputs for PyRx.

• Students will differentiate between good binding and poor binding in PyRx.

• Students will modify a ligand to increase binding affinity to the target protein.

• Students will visualize the ligand-protein results from PyRx and identify key interactions that stabilize binding.

• Students will compare the ligand binding pocket suggested by PyRx with the ligand binding pocket suggested by LigPlot+.

Computational science is an increasingly important part of biochemistry. In this lesson, students are taught to use a popular molecular docking software program to probe the function of a protein of unknown function. Students use the PyRx program to run a docking experiment using AutoDock Vina. They analyze the binding affinities calculated and visualize their results with molecular visualization software. This activity aims to increase students’ knowledge of computational science, demonstrate how computational modeling can be a companion to wet lab experiments, and teach students how to interpret results from computational modeling.

Module Resources

Download student module here

Key Points

• Noncovalent interactions stabilize the binding of ligands to macromolecules like proteins.

• Ligand binding is complex; chemical modifications to a ligand may not result in changes to the interaction energy due to competing stabilizing and destabilizing interactions.