ChEMBL is probably the foremost manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. This script enables you to search ChEMBL directly from StarDrop, returning the data pre-formatted and ready to use for tasks such as:
- Identifying potential off-target activities for your compounds
- Understanding SAR around your compounds or targets
- Building QSAR models to make predictions for new compounds
Please note that any compound structures and target information used in a query will be passed to the ChEMBL servers. These data will be sent using a secure connection (i.e. encrypted and transmitted via HTTPS) and you can view the ChEMBL Data Protection Policy.
Version
This integration is available to use with StarDrop 7.3, 7.4, and 7.5 (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 (7.2 and earlier), please contact us at [email protected] and we will be happy to help install this script on your StarDrop client.
Installing and using the ChEMBL Plug-in for StarDrop
To install this script on Windows:
- Exit StarDrop
- Download the appropriate file for your StarDrop client:
- For StarDrop 7.3 or 7.4: StarDrop Script – ChEMBLWebServices (64-bit).exe
- For StarDrop 7.5: StarDrop Script – ChEMBLWebServices (64-bit)_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
To install this script on macOS:
- Exit StarDrop
- Download the appropriate file for your StarDrop client:
- For StarDrop 7.3 or 7.4: StarDrop Script – ChEMBL (OSX).zip
- For StarDrop 7.5: StarDrop Script – ChEMBL (OSX)_py3Qt.zip
- Extract the contents of the zip file, and within the resulting folder, you should see the following folders:
py3/CheMBL
py3/Utils
site-packages
widgetplugins - 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
Using the ChEMBL Plug-in
After following the installation instructions and restarting StarDrop, you will find a menu item ChEMBL under the Custom Scripts menu in StarDrop. This will give you access to three approaches you can use to search ChEMBL.
Search by ChEMBL Target ID
This option enables you to search for compound activity data associated with a given target. The ChEMBL Target ID is a unique identifier given to each molecular target in the ChEMBL database and you can search for a target in the ChEMBL
web interface to find the ChEMBL Target ID.
The types of assay in which you can search are divided into two broad categories: “Binding Assays” and “Functional and other assays”. For more information on assay types, please see the notes below.
After choosing the assay type, you can specify a list of up to three ChEMBL Target IDs and click the OK button to begin the search.
The search will return a data set in which the first two columns display the structure and ChEMBL Molecule ID for every compound where there is a measured activity against the ChEMBL Target ID(s) entered. The target name and organism will also be displayed in the next two columns.
Following this, for Binding assays, aggregated and filtered pChEMBL values will be displayed for each data type for which an unqualified measurement has been reported (e.g. IC50, Ki, KD). Finally, for each measurement type and unit (e.g. IC50 in μM), two columns are displayed containing aggregated and filtered values (see notes below) for that specific type and unit of data along with links to the corresponding assays descriptions in ChEMBL.
The data for Functional and other assays are more heterogeneous and therefore only columns containing the aggregated and filtered values for each specific type and unit of data, along with links to the corresponding assay descriptions in ChEMBL, are displayed.
These searches can sometimes take a long time to complete due to there being many results. You can stop the search at any time by closing the progress dialogue, at which point any results already retrieved will be displayed in a StarDrop data set.
Search by Similarity to Selected Compound
This option enables you to search for compounds in ChEMBL that are similar to a selected compound in your data set. Before choosing this option, please select a row within your data set.
The types of assay are again divided into two broad categories: “Binding Assays” and “Functional and other assays”. For more information on assay types, please see the notes below.
After choosing an option, you will be prompted to enter a similarity value (between 0.7 and 1). Click the OK button to begin the search.
Any compounds in ChEMBL with greater similarity to the selected compound than the value specified will be returned in a new data set, along with the ChEMBL Molecule ID and the similarity value. Following these will be columns summarising the measured activities against each target for which data are available for any of the similar compounds found.
For Binding assays, aggregated and filtered pChEMBL values will be displayed for each target for which an unqualified measurement has been reported (e.g. IC50, Ki, KD). Finally, for each measurement type and unit (e.g. IC50 in μM) for each target, two columns will be displayed containing aggregated and filtered values (see notes below) for that specific type and unit of data and, along with links to the corresponding assays descriptions in ChEMBL.
The data for Functional and other assays are more heterogeneous and therefore only columns containing the aggregated and filtered values for each specific type and unit of data, along with links to the corresponding assay descriptions in ChEMBL, are displayed.
These searches can sometimes take a long time to complete, particularly for lower similarity values. You can stop the search at any time by closing the progress dialogue, at which point any results already retrieved will be displayed in a StarDrop data set.
Add ChEMBL Molecule IDs to Data Set
This option will search for each structure in your data set and, if the compound exists within the ChEMBL database, return the corresponding ChEMBL Molecule ID. The ChEMBL ID(s) for each compound, if present, will be added as a new column in your data set. Each ID is linked to the corresponding record on the ChEMBL web site.
Notes on Data Returned
Assay Type
When you search by ChEMBL Target ID or using a selected compound, you can choose the assay types to search, either “Binding” or “Functional and other” (all others). These assay types are summarized in the excerpt from the ChEMBL documentation below.
What is the Assay Type?
Binding (B) – Data measuring binding of compound to a molecular target, e.g. Ki, IC50, Kd.
Functional (F) – Data measuring the biological effect of a compound, e.g. % cell death in a cell line, rat weight.
ADMET (A) – ADME data e.g. t1/2, oral bioavailability.
Toxicity (T) – Data measuring toxicity of a compound, e.g., cytotoxicity.
Physicochemical (P) – Assays measuring physicochemical properties of the compounds in the absence of biological material e.g., chemical stability, solubility.
Unclassified (U) – A small proportion of assays cannot be classified into one of the above categories e.g., ratio of binding vs efficacy.
Filtering and Aggregation Rules
Where there are multiple bioactivity or pChEMBL valuesfor a target of the same type (e.g. IC50 or Ki) and units, the result displayed will be the arithmetic mean of the values. When averaging data which contains qualifiers (i.e. <, >, ≤, ≥), a null value will be shown unless the qualifiers are the same on each measurement.