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Find Similar Compounds in PubChem, ChEMBL or the PDB

May 16, 2022

Find Similar Compounds in PubChem, ChEMBL or the PDB

May 16, 2022

This script provides the ability to search PubChem, ChEMBL or the PDB for similar compounds.

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 for assistance.

To install this script on Windows:

  • Ensure that you have saved your work and close StarDrop
  • Download the file StarDrop Script – Find Similar Compounds.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 – Find Similar Compounds.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 – Find Similar Compounds.zip into this folder overwriting any existing files
  • You should now see a folder called Find Similar Compounds
  • Start StarDrop

For StarDrop 7.2 or earlier please use the following files:
On Windows – Download the file StarDrop Script – Find Similar Compounds_py2.exe
On macOS or Windows – Download the file StarDrop Script – Find Similar Compounds_py2.zip

To use this script…

…select one or more rows in your data set and then click on the Custom Scripts->Find Similar Compounds menu item in StarDrop. From the menu, choose whether to search in PubChem, ChEMBL or the PDB. A dialogue box will appear prompting you to specify a similarity level – all compounds with a similarity above this will be returned which is why a high value is recommended for ChEMBL and PubChem in particular. The chosen database will then be searched and a new column added to your adta set with hyperlinks to the compounds found. You will be prompted to indicate whether you would like a new dataset created containing the compounds found.