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The ChEMBL bioactivity database: an update

A. Patrícia Bento, Anna Gaulton, Anne Hersey, Louisa J. Bellis, Jon Chambers, Mark Davies, Felix A. Krüger, Yvonne Light, Lora Mak, Shaun McGlinchey, Michal Nowotka, George Papadatos (+2 others)
2013 Nucleic Acids Research  
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 Nucleic Acids Research Database Issue.  ...  Finally, access to ChEMBL is now available via a new Resource Description Framework format, in addition to the web-based interface, data downloads and web services.  ...  INTRODUCTION ChEMBL is an open large-scale bioactivity database containing information largely manually extracted from the medicinal chemistry literature.  ... 
doi:10.1093/nar/gkt1031 pmid:24214965 pmcid:PMC3965067 fatcat:ndvcr7h2d5grdntilmpuyxrks4

The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data

Mahendra Awale, Jean-Louis Reymond
2017 Journal of Cheminformatics  
PPB searches through 4613 groups of at least 10 same target annotated bioactive molecules from ChEMBL and returns a list of predicted targets ranked by consensus voting scheme and p value.  ...  Several web-based tools have been reported recently which predict the possible targets of a small molecule by similarity to compounds of known bioactivity using molecular fingerprints (fps), however predictions  ...  Funding This work was supported financially by the University of Berne, the Swiss National Science Foundation and the NCCR TransCure.  ... 
doi:10.1186/s13321-017-0199-x pmid:28270862 pmcid:PMC5319934 fatcat:ystfi5b4a5cezczi2ofggrwum4

DrugCentral 2018: an update

Oleg Ursu, Jayme Holmes, Cristian G Bologa, Jeremy J Yang, Stephen L Mathias, Vasileios Stathias, Dac-Trung Nguyen, Stephan Schürer, Tudor Oprea
2018 Nucleic Acids Research  
The web interface has been updated to display and query new data. The full database dump and data files are available for download from the DrugCentral website.  ...  New and existing entries have been updated with the latest information from scientific literature, drug labels and external databases.  ...  ., for contributions to the front-end website development of DrugCentral. FUNDING  ... 
doi:10.1093/nar/gky963 pmid:30371892 pmcid:PMC6323925 fatcat:adbxxj73trgpph4k4f5wnubuvy

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

Eelke B. Lenselink, Niels ten Dijke, Brandon Bongers, George Papadatos, Herman W. T. van Vlijmen, Wojtek Kowalczyk, Adriaan P. IJzerman, Gerard J. P. van Westen
2017 Journal of Cheminformatics  
The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches.  ...  Finally, using an ensemble of DNNs, alongside additional tuning, enhanced the relative performance by another 27% (compared with unoptimized 'DNN_PCM').  ...  Acknowledgements The authors would like to acknowledge NVIDIA and Mark Berger for generously contributing the GPUs.  ... 
doi:10.1186/s13321-017-0232-0 pmid:29086168 pmcid:PMC5555960 fatcat:2fxyq3izrzcznjhau42v7xtkpu

Chemical Entities of Biological Interest: an update

Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, Christoph Steinbeck
2009 Nucleic Acids Research  
ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.  ...  The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge the contribution of the following people to the success of the project: Michael  ... 
doi:10.1093/nar/gkp886 pmid:19854951 pmcid:PMC2808869 fatcat:phtdfvxygrhczfberkbzgmyvyy

PubChem's BioAssay Database

Y. Wang, J. Xiao, T. O. Suzek, J. Zhang, J. Wang, Z. Zhou, L. Han, K. Karapetyan, S. Dracheva, B. A. Shoemaker, E. Bolton, A. Gindulyte (+1 others)
2011 Nucleic Acids Research  
The PubChem BioAssay database currently contains 500 000 descriptions of assay protocols, covering 5000 protein targets, 30 000 gene targets and providing over 130 million bioactivity outcomes.  ...  In this work, we provide an update for the PubChem BioAssay resource, including information content growth, data model extension and new developments of data submission, retrieval, analysis and download  ...  ACKNOWLEDGEMENTS We thank the ChEMBL team at the European Bioinformatics Institute for their assistance with integrating ChEBML data into PubChem.  ... 
doi:10.1093/nar/gkr1132 pmid:22140110 pmcid:PMC3245056 fatcat:trhrxofa6vgojb7gspoxic2rzq

NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity

Alan C. Pilon, Marilia Valli, Alessandra C. Dametto, Meri Emili F. Pinto, Rafael T. Freire, Ian Castro-Gamboa, Adriano D. Andricopulo, Vanderlan S. Bolzani
2017 Scientific Reports  
Consequently, an increase in the effects associated with climatic and ecological changes has been observed in addition to the loss of an arsenal of high-value metabolites 5, 6, 9, 10 .  ...  Since its creation in 2013, the NuBBE DB has changed considerably in terms of content and computational layout, necessitating a report of updated information on these achievements and results.  ...  The database structure was also improved such that data are inserted in a homogeneous and standardized manner, reducing errors. We consider data quality to be an important factor in the NuBBE DB .  ... 
doi:10.1038/s41598-017-07451-x pmid:28775335 pmcid:PMC5543130 fatcat:5ehlcx2yyvazhheqx5azetaaha

The ChEMBL database in 2017

Anna Gaulton, Anne Hersey, Michał Nowotka, A. Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J. Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman (+6 others)
2016 Nucleic Acids Research  
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues.  ...  Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database.  ...  DATA ACCESS The ChEMBL interface The ChEMBL database is accessible via a basic user interface at: https://www.ebi.ac.uk/chembl.  ... 
doi:10.1093/nar/gkw1074 pmid:27899562 pmcid:PMC5210557 fatcat:uez6qoho6nbxzpuncsk4w3juou

canSAR: an updated cancer research and drug discovery knowledgebase

Joseph E. Tym, Costas Mitsopoulos, Elizabeth A. Coker, Parisa Razaz, Amanda C. Schierz, Albert A. Antolin, Bissan Al-Lazikani
2015 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank Prof. Paul Workman for input and many helpful discussions. They are extremely grateful to their many collaborators and data providers, the full list of whom  ...  For example, 3D structure data (3) and canSAR's structurebased druggability (4) calculations are updated weekly; while data from the ChEMBL (5) database are typically 1-2 weeks after the ChEMBL update.  ...  The data in canSAR are updated at regular intervals as dictated by the data type.  ... 
doi:10.1093/nar/gkv1030 pmid:26673713 pmcid:PMC4702774 fatcat:gjjqpzab5vebvdxa3lslrdlfjq

Retrieving GPCR data from public databases

Christopher Southan
2016 Current opinion in pharmacology (Print)  
Ensembl for genes, ChEMBL for bioactive chemistry and SureChEMBL for patents.  ...  The former has an emphasis on structures, sequences, point mutations, analysis tools and visualisation.  ...  Primary Databases Primary databases are associated with the direct deposition of experimental data at large scale. They rely heavily on automated annotation and are updated frequently.  ... 
doi:10.1016/j.coph.2016.07.002 pmid:27472010 fatcat:tuoiywzl7rbzleusjkm5n3ihly

TIMBAL v2: update of a database holding small molecules modulating protein–protein interactions

Alicia P. Higueruelo, Harry Jubb, Tom L. Blundell
2013 Database: The Journal of Biological Databases and Curation  
ChEMBL database; Adrian Schreyer for maintenance of the local copy of ChEMBL  ...  Acknowledgements The authors thank Colin Groom for his encouragement to include stabilisers of protein complexes as well as their inhibitors; John Overington and Yvonne Light for their support with the  ...  The resource will be updated with each new release of the ChEMBL database.  ... 
doi:10.1093/database/bat039 pmid:23766369 pmcid:PMC3681332 fatcat:nhdt3qlvzreolfcwadipgz2a6u

ChEMBL: a large-scale bioactivity database for drug discovery

A. Gaulton, L. J. Bellis, A. P. Bento, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, D. Michalovich, B. Al-Lazikani, J. P. Overington
2011 Nucleic Acids Research  
ChEMBL is an Open Data database containing binding, functional and ADMET information for a large number of drug-like bioactive compounds.  ...  Currently, the database contains 5.4 million bioactivity measurements for more than 1 million compounds and 5200 protein targets.  ...  We also greatly appreciate and acknowledge the feedback from users on data content and organization of the database.  ... 
doi:10.1093/nar/gkr777 pmid:21948594 pmcid:PMC3245175 fatcat:adyfi5w7obgoheqg6jkm3os47y

StreptomeDB 3.0: an updated compendium of streptomycetes natural products

Aurélien F A Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A Kirchner, Bakoh Ndingkokhar, Boris D Bekono, Conrad V Simoben, Smith B Babiaka, Yvette I Malange, Florian Sauter, Paul Zierep (+2 others)
2020 Nucleic Acids Research  
Antimicrobial resistance is an emerging global health threat necessitating the rapid development of novel antimicrobials.  ...  Initially released in 2012, StreptomeDB (http://www.pharmbioinf.uni-freiburg.de/streptomedb) is the first and only public online database that enables the interactive phylogenetic exploration of streptomycetes  ...  ACKNOWLEDGEMENTS We thank the many users of StreptomeDB for their feedback.  ... 
doi:10.1093/nar/gkaa868 pmid:33051671 fatcat:6fcj4n66qrfd5ncu6r6vbv4gse

ChemProt-3.0: a global chemical biology diseases mapping

Jens Kringelum, Sonny Kim Kjaerulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
2016 Database: The Journal of Biological Databases and Curation  
In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19 504 proteins.  ...  In addition, the user has the possibility to search by compound, target, pathway, disease and clinical effect.  ...  Data sources We updated all the chemical protein interactions data from the open source databases ChEMBL (version 19) (4), BindingDB (17) , PDSP Ki database (18) , DrugBank (version 4) (19) , PharmGKB  ... 
doi:10.1093/database/bav123 pmid:26876982 pmcid:PMC4752971 fatcat:rvrdyvwbo5eebp3d5zylcvelwu

Public Domain Databases for Medicinal Chemistry

George Nicola, Tiqing Liu, Michael K. Gilson
2012 Journal of Medicinal Chemistry  
binding and bioactivity, BindingDB, ChEMBL and PubChem, and noting as well several other small molecule databases that are also of great value.  ...  Databases of small molecule binding and bioactivity This section is intended to help medicinal chemists understand and start using BindingDB, ChEMBL and/or PubChem.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health or the European Commission.  ... 
doi:10.1021/jm300501t pmid:22731701 pmcid:PMC3427776 fatcat:dzbzfdturrb7lljocuu6s3ht3y
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