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Course A

Title: Different ways to run Receptor-ligand molecular docking using AutoDock Vina

Abstract: In this course we will present different ways to perform receptor-ligand molecular docking using the software AutoDock Vina. We begin by exploring molecular docking considering the following configurations: (i) one or many ligands; (ii) one or many receptor structures and (iii) one grid box or different grid boxes. We will also introduce different approaches to incorporate protein flexibility in molecular docking, with a focus on the one considering the results of a molecular dynamics simulation. Furthermore, we are going to present a framework for virtual screening that permits to configure distinct ways of running molecular docking experiments. Finally, we will discuss the impact of AutoDock Vina parameters, namely grid box size and exhaustiveness, on the docking experiments.

Instructors:

Karina Machado (FURG)  Adriano Werhli (FURG)