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).
Version
This integration is available to use with StarDrop 7.4 and 7.5 for either Windows or Mac. 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 (7 and earlier), please contact us at support@optibrium.com and we will be happy to help installing this script on your StarDrop client.
Installing and using the AtlasCBS script for StarDrop
- Exit StarDrop
- Download the appropriate file for your StarDrop client:
- For StarDrop 7.3 or 7.4: StarDrop Script – AtlasCBS.exe
- For StarDrop 7.5: StarDrop Script – AtlasCBS_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 the appropriate file for your StarDrop client:
- For StarDrop 7.3 or 7.4: StarDrop Script – AtlasCBS.zip
- For StarDrop 7.5: StarDrop Script – AtlasCBS_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/AtlasCBS
py3/Utils - Start StarDrop
- Exit StarDrop
- Download the appropriate file for your StarDrop client:
- For StarDrop 7.3 or 7.4: StarDrop Script – AtlasCBS.zip
- For StarDrop 7.5: StarDrop Script – AtlasCBS_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/AtlasCBS
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 AtlasCBS script for StarDrop
Please 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.