https://github.com/chembl/compound_target_pairs_dataset
Automatic extraction of interacting compound-target pairs from ChEMBL.
https://github.com/chembl/compound_target_pairs_dataset
chembl cheminformatics chemistry chemoinformatics dataset drug-target-interactions drug-targets python
Last synced: 4 months ago
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Automatic extraction of interacting compound-target pairs from ChEMBL.
- Host: GitHub
- URL: https://github.com/chembl/compound_target_pairs_dataset
- Owner: chembl
- License: apache-2.0
- Created: 2022-10-13T13:22:59.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-09-23T13:28:48.000Z (9 months ago)
- Last Synced: 2025-09-23T15:33:15.334Z (9 months ago)
- Topics: chembl, cheminformatics, chemistry, chemoinformatics, dataset, drug-target-interactions, drug-targets, python
- Language: Python
- Homepage:
- Size: 4.11 MB
- Stars: 17
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
Dataset of Interacting Compound-Target Pairs in ChEMBL
# Introduction
This code extracts a dataset of compound-target pairs from the open-source bioactivity database [ChEMBL](https://www.ebi.ac.uk/chembl/) [Zdrazil2023].
The compound-target pairs are known to interact because
- they have at least one corresponding measured activity value in ChEMBL or
- they are part of a set of manually curated known interactions in ChEMBL.
Furthermore, the dataset contains a number of compound and target annotations to enable future analyses.
Previously, a similar dataset has been curated manually and has been used to investigate target-based differences in drug-like properties and ligand efficiencies [Leeson2021].
This code can generate an extended version of the previous dataset for every ChEMBL version from ChEMBL 26 onwards.
[Zdrazil2023]: Zdrazil et al., "The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods",
Nucleic Acids Research, gkad1004, 2023, https://doi.org/10.1093/nar/gkad1004
[Leeson2021]: Leeson et al., "Target-Based Evaluation of “Drug-Like” Properties and Ligand Efficiencies",
Journal of Medicinal Chemistry, 64(11), 7210-7230, 2021, https://doi.org/10.1021/acs.jmedchem.1c00416
# Dataset
The dataset for different ChEMBL versions from ChEMBL 26 onwards is available [here](https://ftp.ebi.ac.uk/pub/databases/chembl/Drug_Target_dataset/).
# Quick Start
## Dependencies
Install the required dependencies with
```
pip install .
```
Note: Using Pandas version 2.2 will lead to warnings regarding the RDKit PandasTools when running the code.
However, the final dataset is not impacted.
## Generating the Dataset
The default version of the dataset (the full dataset as a CSV file based on the newest ChEMBL version) can be generated by calling
```
python main.py -o
```
An overview of the available arguments to modify the output is available by calling
```
python main.py --help
```
## Documentation
The full documentation is available [here](https://chembl.github.io/compound_target_pairs_dataset/).
The corresponding article is available [here](https://doi.org/10.1038/s41597-024-03582-9).