Introduction

Aims

AFVS is one of the modules of AdaptiveFlow, dedicated to carrying out the virtual screening procedures.

This tutorial will demonstrate the following:

1. How AFVS can be installed

2. How the ATG Prescreen is prepared

3. How the ATG Prescreen is started

4. How the ATG Prescreen is monitored

5. How the ATG Prescreen is postprocessed

6. How the ATG Primary Screen is prepared

7. How the ATG primary screen is started

8. How the ATG primary screen is postprocessed

This tutorial covers the basic functionality of AFVS. Further information regarding specific aspects of AFVS can be found in the documentation.

The Target

The target structure in this tutorial is human glucokinase (GK), and the purpose of the screening is to find activating compounds (see Petit et al. for background information). The structure used has the following protein data bank identification (PDB ID): 4NO7 (https://www.rcsb.org/structure/4NO7).

Docking Scenarios

The files in this tutorial come with two pre-configured docking scenarios:

1. QuickVina 2 with exhaustiveness set to 1

2. Smina Vinardo with exhaustiveness set to 1

All other docking parameters are the same for both docking programs.

The pre-configured docking box is shown below:

Details on how to prepare the docking input files for Autodock Vina-based programs can for example be found at http://vina.scripps.edu.