Virtual Libraries for Docking Methods: Guidelines for the Selection and the Preparation

Prior to any docking study, the virtual compounds database that will be screened must be carefully selected and prepared. This compound collection, often referred to as the virtual library, can encompass up to millions of compounds. Already prepared virtual libraries can be used, but users can also generate their own. In this chapter, we will present the different categories of virtual screening libraries together with guidelines for their preparation prior to docking. We will present the different categories of compound collections and we will distinguish actual and virtual compounds databases. We will then describe the key steps for virtual library preparation by detailing the database cleaning and discussing the use of ADME/Tox filters.