Introduction

This is the first tutorial for VirtualFlow for Virtual Screening (VFVS).

Aims

The goals of this tutorial are to demonstrate:

1. How VFVS can be installed (in a preconfigured setting)

2. How the workflow prepared (in a preconfigured setting)

3. How VFVS is principally used:

   1. Starting the workflow

   2. Monitoring the workflow

4. How to obtain the output database after completion

This is a short tutorial, which only covers some of the basics.

The Target

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

Human glucokinase (GK). The structure shown has PDB ID 4NO7.

Docking Scenarios

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

1. QuickVina 2 with exhaustiveness set to 8
2. Smina Vinardo with exhaustiveness set to 4

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.