> For the complete documentation index, see [llms.txt](https://docs.virtual-flow.org/tutorials-vf1/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.virtual-flow.org/tutorials-vf1/vfvs-tutorial-1-bash/introduction.md).

# 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](/tutorials-vf1/vfvs-tutorial-1-bash/installation.md) (in a preconfigured setting)
2. [How the workflow prepared ](/tutorials-vf1/vfvs-tutorial-1-bash/setting-up-the-workflow.md) (in a preconfigured setting)
3. How VFVS is principally used:
   1. [Starting the workflow](/tutorials-vf1/vfvs-tutorial-1-bash/starting-the-workflow.md)
   2. [Monitoring the workflow](/tutorials-vf1/vfvs-tutorial-1-bash/monitoring-the-workflow.md)
4. [How to obtain the output database after completion](/tutorials-vf1/vfvs-tutorial-1-bash/the-completed-workflow.md)

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.*](http://scripts.iucr.org/cgi-bin/paper?S0907444911036729) for background information). The structure used has PDB ID 4NO7 (<https://www.rcsb.org/structure/4NO7>).&#x20;

![Human glucokinase (GK). The structure shown has PDB ID 4NO7.](https://2448761891-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-La7DYI9bRcHy2XQUx5L%2F-LaFe4sXOhA_x0oD02oK%2F-LaFgYvo9yOOkI_PWp90%2FScreenshot%20at%202019-03-18%2008-06-11.png?alt=media\&token=94eb2985-79dd-4cc7-b2af-e9d1d9c356d9)

## Docking Scenarios

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

1. [QuickVina 2](https://academic.oup.com/bioinformatics/article/31/13/2214/195750) with exhaustiveness set to 8
2. [Smina Vinardo](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155183) with exhaustiveness set to 4

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

The pre-configured docking box is shown below:

![](https://2448761891-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-La7DYI9bRcHy2XQUx5L%2F-LaFe4sXOhA_x0oD02oK%2F-LaFhzkHkEIAytGjSySQ%2FScreenshot%20at%202019-03-18%2008-02-56.png?alt=media\&token=d6de591c-2f9e-4cd0-a5de-80c7c2e2ab1e)

![](https://2448761891-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-La7DYI9bRcHy2XQUx5L%2F-LaFe4sXOhA_x0oD02oK%2F-LaFi26M-zGapeab6CSP%2FScreenshot%20at%202019-03-18%2008-03-10.png?alt=media\&token=29d85987-27e4-497a-9999-dd77af560e03)

![](https://2448761891-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-La7DYI9bRcHy2XQUx5L%2F-LaFe4sXOhA_x0oD02oK%2F-LaFi86LZzT210aiXkqJ%2FScreenshot%20at%202019-03-18%2008-03-18.png?alt=media\&token=bea40b50-e29c-486a-9a7a-72ea7ba5d92a)

Details on how to prepare the docking input files for Autodock Vina-based programs can for example be found at [http://vina.scripps.edu](http://vina.scripps.edu/).&#x20;