{"id":44355134,"url":"https://github.com/chembl/compound_target_pairs_dataset","last_synced_at":"2026-02-11T16:05:03.798Z","repository":{"id":224959827,"uuid":"550876229","full_name":"chembl/compound_target_pairs_dataset","owner":"chembl","description":"Automatic extraction of interacting compound-target pairs from 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chembl","cheminformatics","chemistry","chemoinformatics","dataset","drug-target-interactions","drug-targets","python"],"created_at":"2026-02-11T16:05:03.015Z","updated_at":"2026-02-11T16:05:03.785Z","avatar_url":"https://github.com/chembl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1 align=\"center\"\u003e\n    Dataset of Interacting Compound-Target Pairs in ChEMBL\n\u003c/h1\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://zenodo.org/doi/10.5281/zenodo.10723114\"\u003e\u003cimg src=\"https://zenodo.org/badge/550876229.svg\" alt=\"Code DOI\"\u003e\u003c/a\u003e\n    \u003ca href=\"https://doi.org/10.5281/zenodo.10721939\"\u003e\u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.10721939.svg\" alt=\"Dataset DOI\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n# Introduction\nThis code extracts a dataset of compound-target pairs from the open-source bioactivity database [ChEMBL](https://www.ebi.ac.uk/chembl/) [Zdrazil2023]. \n\nThe compound-target pairs are known to interact because \n\n- they have at least one corresponding measured activity value in ChEMBL or \n- they are part of a set of manually curated known interactions in ChEMBL.\n\nFurthermore, the dataset contains a number of compound and target annotations to enable future analyses. \n\nPreviously, a similar dataset has been curated manually and has been used to investigate target-based differences in drug-like properties and ligand efficiencies [Leeson2021]. \nThis code can generate an extended version of the previous dataset for every ChEMBL version from ChEMBL 26 onwards.  \n\n[Zdrazil2023]: Zdrazil et al., \"The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods\",\n    Nucleic Acids Research, gkad1004, 2023, https://doi.org/10.1093/nar/gkad1004\n\n[Leeson2021]: Leeson et al., \"Target-Based Evaluation of “Drug-Like” Properties and Ligand Efficiencies\", \n    Journal of Medicinal Chemistry, 64(11), 7210-7230, 2021, https://doi.org/10.1021/acs.jmedchem.1c00416\n\n# Dataset\nThe dataset for different ChEMBL versions from ChEMBL 26 onwards is available [here](https://ftp.ebi.ac.uk/pub/databases/chembl/Drug_Target_dataset/).\n\n# Quick Start\n## Dependencies\nInstall the required dependencies with\n```\npip install .\n```\n\nNote: Using Pandas version 2.2 will lead to warnings regarding the RDKit PandasTools when running the code. \nHowever, the final dataset is not impacted. \n\n\n## Generating the Dataset\nThe default version of the dataset (the full dataset as a CSV file based on the newest ChEMBL version) can be generated by calling \n```\npython main.py -o \u003coutput_path\u003e\n```\n\nAn overview of the available arguments to modify the output is available by calling \n\n```\npython main.py --help\n```\n\n## Documentation\nThe full documentation is available [here](https://chembl.github.io/compound_target_pairs_dataset/).\n\nThe corresponding article is available [here](https://doi.org/10.1038/s41597-024-03582-9).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchembl%2Fcompound_target_pairs_dataset","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchembl%2Fcompound_target_pairs_dataset","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchembl%2Fcompound_target_pairs_dataset/lists"}