ChEMBL: towards direct deposition of bioassay data

By David Mendez, Anna Gaulton, A. P. Bento, Jon Chambers, M. D. Veij, Eloy Felix, M. P. Magariños, J. F. Mosquera, Prudence Mutowo-Meullenet, M. Nowotka and 11 more. 2018

2,013 citations recorded by the source corpus.

Abstract ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

GPCRdb in 2021: integrating GPCR sequence, structure and function (2020, methodology): “All GPCR ligands and their biological activities were imported from ChEMBL version 27 (21) using the ChEMBL web services (22) which were queried using ChEMBL identifiers.”
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets (2022, background): “, ChEMBL [21], ChEBI [22], DrugBank [23], BindingDB [24], PharmGKB [25], Guide to Pharmacology [26], Selleck, and ZINC [27]), and drug target profiles from MICHA [28].”
Mapping the Landscape of Artificial Intelligence Applications against COVID-19 (2020, methodology): “The model is ﬁrst trained on 1.6 million molecules from the ChEMBL database (Davies et al., 2015; Mendez et al., 2019), and then adapted to a smaller dataset of protease inhibitors using transfer learning.”
TCM network pharmacology: A new trend towards combining computational, experimental and clinical approaches. (2021, neutral): “MD-Miner Identify patient-specific potential drugs 2017 [40]”
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts (2020, methodology): “Drug claims from DGIdb were normalized using the ChEMBL and Wikidata normalizers from thera-py .”
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt (2022, methodology): “In parallel, a ML model is used to expand the list of drug indications by mining drug labels (11).”
ProTox 3.0: a webserver for the prediction of toxicity of chemicals (2024, methodology): “Data on cardiotoxic and non-cardiotoxic chemical compounds a dataset of 5252 compounds with hERG inhibition values (IC50 and Ki) was obtained from the ChEMBL database ( 24 ).”
Artificial intelligence to deep learning: machine intelligence approach for drug discovery (2021, background): “Further, the ChEMBL database (https:// www. ebi. ac. uk/ chembl/) [56] is an open access big database containing data of numerous bioactive compounds exhibiting drug-like properties [57].”
Chemformer: a pre-trained transformer for computational chemistry (2021, positive): “Chemformer’s vocabulary is constructed by applying regular expression matching (we use the same regex as the Molecular Transformer [4]) to the canonical SMILES of the molecules in the ChEMBL 27 [36].”
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities (2019, background): “uk/chembl/ [40] ChemIDplus 2 https://chem.”
A practical guide to large-scale docking (2021, background): “For a given target, these can be found in the scienti ﬁ c literature, patent literature or public databases such as IUPHAR/BPS 114 , ChEMBL 115 or ZINC 9,99,116 , or available in-house.”
QMugs, quantum mechanical properties of drug-like molecules (2022, neutral): “The assignment of ChEMBL identifiers to tarballs is described in a tarball_assignment.csv file.”
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources (2022, methodology): “The Ligands subsection of GPCRdb has been extended to 211 320 ligands and 466 278 binding affinity or potency values from the ChEMBL (16), Guide to Pharmacology (15) or PDSP Ki databases (https://pdsp.”
ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support (2024, positive): “We incorporated a wide spectrum of open-access bioactivity databases including ChEMBL ( 16 ), PubChem ( 17 ) and OCHEM ( 18 ), as well as rigorously peer-reviewed literature ( 19–24 ).”