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  • Tutorial Overview
  • Tutorial 1: VFVS 2.0 on AWS
    • Introduction
    • Installation of VFVS
    • Setting up the ATG Prescreen
    • Starting the ATG Prescreen
    • Monitoring the ATG Prescreen
    • Postprocessing the ATG Prescreen
    • Preparing the ATG Primary Screen
    • Running the ATG Primary Screen
    • Postprocessing the ATG Primary Screen
  • Tutorial 2: VFVS 2.0 on Slurm
    • Introduction
    • Installation of VFVS
    • Setting up the ATG Prescreen
    • Starting the ATG Prescreen
    • Monitoring the ATG Prescreen
    • * Postprocessing the ATG Prescreen
    • Preparing the ATG Primary Screen
    • Running the ATG Primary Screen
    • * Postprocessing the ATG Primary Screen
    • The Completed Workflow (Update in Progress for the Python version)
      • Local installation and deployment of HPC-toolkit
      • Installing VirtualFlow2.0
      • Screening the sparse library with VirtualFlow 2.0
      • Extracting and viewing the results
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  • Aims
  • The Target
  • Docking Scenarios
  1. Tutorial 1: VFVS 2.0 on AWS

Introduction

This is the first tutorial for VirtualFlow for Virtual Screening 2.0 (VFVS 2.0).

PreviousTutorial OverviewNextInstallation of VFVS

Last updated 1 year ago

Aims

VFVS is one of the modules of VirtualFlow, dedicated to carrying out the virtual screening procedures.

This tutorial will demonstrate the following:

This tutorial covers the basic functionality of VFVS 2.0. Further information regarding specific aspects of VFVS can be found in the .

The Target

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

Docking Scenarios

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

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

The pre-configured docking box is shown below:

with exhaustiveness set to 1

with exhaustiveness set to 1

Details on how to prepare the docking input files for Autodock Vina-based programs can for example be found at .

QuickVina 2
Smina Vinardo
http://vina.scripps.edu
How VFVS 2.0 can be installed
How the ATG Prescreen is prepared
How the ATG Prescreen is started
How the ATG Prescreen is monitored
How the ATG Prescreen is postprocessed
How the ATG Primary Screen is prepared
How the ATG primary screen is started
How the ATG primary screen is postprocessed
Petit et al.
https://www.rcsb.org/structure/4NO7
documentation
Human glucokinase (GK). The structure shown has PDB ID 4NO7.