This script provides a method for calculating Ligand Efficiency in StarDrop; a simple quantifiable 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 metric is as follows:
Version
This integration is available to use with the latest version of StarDrop (Windows and macOS). To find out which version you have installed, start StarDrop and select the Help->About menu.
If you are using an older version of StarDrop, please contact us at support@optibrium.com and we will be happy to help install this script on your StarDrop client.
Installing and using the Ligand Efficiency script for StarDrop
- Exit StarDrop
- Download StarDrop Script – Ligand Efficiency_py3Qt.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
- Exit StarDrop
- Download StarDrop Script – Ligand Efficiency_py3Qt.zip
- In your user area, navigate to the StarDrop Python folder in C:\Users\username\AppData\Roaming\StarDrop
- Extract the contents of the zip file into this folder overwriting any existing files
- You should now see the following folders in the StarDrop folder:
py3\Ligand Efficiency
py3\Utils - Start StarDrop
- Exit StarDrop
- Download StarDrop Script – Ligand Efficiency_py3Qt.zip
- Extract the contents of the zip file into this folder overwriting any existing files, you should now see the following folders in the StarDrop folder:
py3\Ligand Efficiency
py3\Utils - In your user area, navigate to the StarDrop folder: /Users/username/StarDrop
- Move the unzipped folders, sub-folders, and files into the StarDrop folder, overwriting any existing files
- Start StarDrop
To use the Ligand Efficiency script
Click on the Custom Scripts->Calculate Ligand Efficiency menu item in StarDrop. If the open data set contains appropriate data, a dialogue box will appear, prompting for a column against which to calculate ligand efficiency values. The data set must include a Structure column and a pKi column. A µ Ki column can be used instead of a pKi column, given the column is formatted accordingly. You can format a column by right-clicking on the column header and selecting the Edit menu option. Once selected, the script will create a new column next to the chosen one with the calculated values.
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.
For support with this script or anything else please reach out to us at support@optibrium.com