Introduction

Druggability Suite is a VMD plugin GUI and a Python module developed for setup and analysis of simulations described in [AB12].

Installation

  1. VMD 1.9.1 or later is required for using GUI. NAMD_ is required for running druggability simulations. Following are required for performing druggability analysis calculations:
  1. Download one of the following archive files:
  1. Extract contents of the archive and copy drugui folder to VMD TCL plugins directory, i.e. $VMDDIR/plugins/noarch/tcl/.

    Then, insert following line into $VMDDIR/scripts/vmd/loadplugins.tcl at line 186:

    vmd_install_extension drugui drugui_tk "Modeling/DruGUI"
    

    If you are not sure where VMD directory is located, run vmd, and type the following command line in the VMD console:

    global env; puts $env(VMDDIR)
    

DruGUI Plugin

Druggability Suite GUI (DruGUI) plugin, shown below, has five panels to streamline setup, analysis, and visualization of druggability simulations:

../../_images/drugui.png

The rest of the tutorial will show you how to use these panels, and described required inputs and outputs from different analysis steps.

Tutorial Files

Files in the following archives can be used to follow this tutorial:

Here is a list of these files:

 3.5K  mdm2_output.log
 592K  mdm2_output.pdb
1003K  mdm2_output.psf
  254  mdm2_output.xsc
 112K  mdm2.pdb
 335K  mdm2.psf
 3.9K  sample_1t4e_inhibitor.pdb
 2.2M  sample_ACAM.dx
 2.2M  sample_ACET.dx
 4.5K  sample_all_hotspots.pdb
  55K  sample_heavyatoms.pdb
 2.2M  sample_IPAM.dx
 2.4M  sample_IPRO.dx
 5.7K  sample.log
 1.3K  sample_site_1.pdb
  553  sample_site_1_soln_1.pdb
  553  sample_site_1_soln_2.pdb
  553  sample_site_1_soln_3.pdb

How to Cite

If you benefited from Druggability Suite in your research, please cite the following paper:

[AB12]Bakan A, Nevins N, Lakdawala AS, Bahar I Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules J Chem Theory Comput 2012 8(7):2435-2447