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Ligand Efficiency

May 16, 2022

Ligand Efficiency

May 16, 2022

This script provides a method for calculating Ligand Efficiency; a simple metric for assessing whether a ligand derives its potency from having an optimal fit with the protein target or simply by virtue of making many contacts.

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 [email protected] for assistance.

To install this script on Windows:

  • Ensure that you have saved your work and close StarDrop
  • Download the file StarDrop Script – Ligand Efficiency.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 – Ligand Efficiency.zip
  • In your user area, navigate to the StarDrop Python folder (on Windows this is in C:\Users\username\AppData\Roaming\StarDrop\py3, on macOS this is in ~/StarDrop/py3)
  • Extract the contents of StarDrop Script – Ligand Efficiency.zip into this folder overwriting any existing files
  • You should now see a folder called Ligand Efficiency 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 – Ligand Efficiency_py2.exe
On macOS or Windows – Download the file StarDrop Script – Ligand Efficiency_py2.zip

To use this script…

…click on the Custom Scripts->Calculate Ligand Efficiency menu item in StarDrop. If there is no data set open (or the open data set has no appropriate data for calculating ligand efficiency) it will give a message saying that there is no data available for calculation. If there is a data set with appropriate data open, a dialogue box will appear prompting for a column against which to calculate ligand efficiency values. Once chosen, the script will create add in a new column next to the chosen one with the calculated values.