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AtlasCBS

May 16, 2022

AtlasCBS

May 16, 2022

This AtlasCBS script, created by Dr Cele Abad-Zapatero of the University of Illinois at Chicago and Alvaro Cortes from the University of Alcala de Henares (Madrid), enables you to explore chemico-biological space using Ligand Efficiency Indices (LEIs) as variables. This unique set of variables enables you to create graphical representations of the content of databases that contain affinity data (SAR databases such as PDBBind, BindingDB) in a map-like environment with different variables and scales. This provides you with two-dimensional charts where the angular coordinate is related to the chemical composition of the ligand(s) and the radial coordinate is related to affinity of the ligand(s) towards the specific target(s).

The installer file and instructions for how to install and use the script are provided in the following pages…

Version

This script is for StarDrop 7.3 for either Windows® or Mac®. To find out which version you have installed, start StarDrop and select the Help->About menu

Installation

We have recently updated StarDrop’s scripting to make it easier for everyone to download and install scripts without needing administrator privileges. If you are already using custom scripts that you downloaded and installed while using a previous version of StarDrop, then you will need to download these again (they have all been updated) and follow the installation instructions. If you are using any in-house scripts to access internal systems or databases, or are uncertain about what to do, then please contact stardrop-support@optibrium.com for assistance.

To install this script on Windows:

  • Ensure that you have saved your work and close StarDrop
  • Download the file StarDrop Script – AtlasCBS.exe
  • When the download is complete, double-click the file to run it and follow the instructions (we recommend that you accept the default options provided)
  • Start StarDrop

To install this script on macOS or Windows:

  • Ensure that you have saved your work and close StarDrop
  • Download the file StarDrop Script – AtlasCBS.zip
  • In your user area, navigate to the StarDrop Python folder (on Windows this is in C:\Users\username\AppData\Roaming\StarDrop\py, on macOS this is in ~/StarDrop/py)
  • Extract the contents of StarDrop Script – AtlasCBS.zip into this folder overwriting any existing files
  • You should now see a folder called AtlasCBS and a folder called Utils
  • Start StarDrop

For StarDrop 7.2 or earlier please use the following files:
On Windows – Download the file StarDrop Script – AtlasCBS_py2.exe
On macOS or Windows – Download the file StarDrop Script – AtlasCBS_py2.zip

To use this script…

…ensure you have opened a data set which contains a column of structures and a column of pKi values. Click on the Custom Scripts->AtlasCBS: Ligand Efficiency Indices menu item in StarDrop. If there is no data set open (or the open data set does not contain any structures) it will give a message saying that the operation is not possible. Once complete, the script will add a series of columns representing different LEIs to your data set. Using StarDrop’s visualisation tools, these variables can be used to create representations of chemico-biological space.