The ChEMBL-og

We are pleased to announce the release of ChEMBL_26 This version of the database, prepared on 10/01/2020 contains: 2,425,876 compound records 1,950,765 compounds (of which 1,940,733 have mol files) 15,996,368 activities 1,221,311 assays 13,377 targets 76,076 documents You can query the ChEMBL 26 data online via the ChEMBL Interface and you can also download the data from the ChEMBL FTP site . Please see ChEMBL_26 release notes for full details of all changes in this release. Changes since the last release: * Deposited Data Sets: CO-ADD antimicrobial screening data: Two new data sets have been included from the Community for Open Access Drug Discovery (CO-ADD). These data sets are screening of the NIH NCI Natural Product Set III in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296183, DOI = 10.6019/CHEMBL4296183) and screening of the NIH NCI Diversity Set V in the CO-ADD assays (src_id = 40, Document ChEMBL_ID = CHEMBL4296182, DOI = 10.601...

We are pleased to announce the release of ChEMBL_20. This version of the database was prepared on 14th January 2015 and contains: 1,715,135 compound records 1,463,270 compounds (of which 1,456,020 have mol files) 13,520,737 activities 1,148,942 assays 10,774 targets 59,610 source documents You can query the ChEMBL 20 data online via the ChEMBL Interface and you can also download the data from the ChEMBL ftpsite . Please see ChEMBL_20 release notes for full details of all changes in this release.   Changes since the last release In addition to the regular updates to the Scientific Literature, PubChem, FDA Orange Book and USP Dictionary of USAN and INN Investigational Drug Names this release of ChEMBL also includes the following new datasets:    AstraZeneca in-vitro DMPK and physicochemical properties AstraZeneca have provided  experimental data on a set of publicly disclosed compounds in the following ADMET related assays : pKa, lipophilic...

Happy New Year for 2015 from the ChEMBL group! Release 20 of the ChEMBL database will be happening around the end of the month, and for those who can't wait, here's a preview of the exciting new features you can expect to find there: HELM notation - we have developed an implementation of the Pistoia Alliance's HELM standard for biotherapeutics and will be supplying HELM notation for just under 20K peptides (previously represented by mol files). We will also make our monomer library available in case others wish to use it to generate their own HELM notation. Structural alerts - in place of the old 'Med Chem Friendly' flag used in ChEMBL, we now have an extensive set of structural alerts calculated for the ChEMBL compounds. The data set includes eight different sets of alerts (including sets published by Pfizer, Glaxo, BMS, University of Dundee, NIH MLSMR and PAINS filters) providing more than 1100 distinct SMARTS. Alerts found for a given compound can be vie...

There are now multiple formats and ways to access the ChEMBL data, and we have recently assigned DOIs to all available versions of ChEMBL (and will archive these on the ftp server, permanently). So when you publish use of ChEMBL, could you reference the following papers: ChEMBL Database A. Gaulton, L. Bellis, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, R. Akhtar, A.P. Bento, B. Al-Lazikani, D. Michalovich, & J.P. Overington (2012) ‘ChEMBL: A Large-scale Bioactivity Database For Chemical Biology and Drug Discovery’ Nucleic Acids Res. Database Issue , 40 D1100-1107. DOI:10.1093/nar/gkr777 PMID:21948594 A.P. Bento, A. Gaulton, A. Hersey, L.J. Bellis, J. Chambers, M. Davies, F.A. Krüger, Y. Light, L. Mak, S. McGlinchey, M. Nowotka, G. Papadatos, R. Santos & J.P. Overington (2014) ‘The ChEMBL bioactivity database: an update’ Nucleic Acids Res . Database Issue , 42 1083-1090. DOI:10.1093/nar/gkt103 PMID: 24214965 myChEMBL R. Ochoa, M. Davies...

We are pleased to announce the release of ChEMBL_19 . This version of the database was prepared on 3rd July 2014 and contains: 1,637,862 compound records 1,411,786 compounds (of which 1,404,752 have molfiles) 12,843,338 bioactivities 1,106,285 bioassays 10,579 targets 57,156 abstracted documents Data can be downloaded from the ChEMBL ftpsite . Please see ChEMBL_19 release notes for full details of the changes in this release. New crop protection data We have now expanded the content of ChEMBL to include data relevant to crop protection research. Bioactivity data covering insecticides, fungicides and herbicides were extracted from a number of different journals such as J. Agric. Food. Chem., J. Pesticide Sci., Crop Protection and Pest Manag. Sci. The addition of this dataset to ChEMBL was funded by Syngenta . In total, more than 40K compound records and 245K activities were added in this dataset. These data are included in the 'Scientific Literature' data so...

We are pleased to announce the release of ChEMBL_18. This version of the database was prepared on 12th March 2014 and contains: 1,566,466 compound records 1,359,508 compounds (of which 1,352,681 have mol files) 12,419,715 activities 1,042,374 assays 9,414 targets 53,298 documents The web front end at https://www.ebi.ac.uk/chembl is now connected to the ChEMBL 18 data, but you can also download the data from the ChEMBL ftpsite . Please see ChEMBL_18 release notes for full details of all changes in this release. Changes since the last release   New data sets   The ChEMBL_18 release includes the following new datasets: University of Vienna G-glycoprotein (pgp) screening data UCSF MMV Malaria Box screening data DNDi Trypanosoma cruzi screening data DrugMatrix in vivo toxicology data In addition, 43,335 new compound records from 2015 publications in the primary literature have been added to this release. Approved drug and usan data have also been...

Many of you will have noticed a new section on the ChEMBL interface, specifically at the Document Report Card page, called Related Documents . It consists of a table listing the links for up to 5 other ChEMBL documents ( i.e. publications aka papers) that are scored to be the most similar to the one featured in the report card. Here's an example .  How does this work? There are examples of related documents sections online, e.g. in PubMed or in various journal publishers' websites. Document 'related-ness' or similarity can be assessed by comparing MeSH keywords or by clustering documents using TF-IDF weighted term vectors. Fortunately, ChEMBL puts a lot of effort in manually extracting and curating the compounds and biological targets from publications, so why not using these as descriptors to assess document similarity instead - as far as we know this is the first time this approach has been implemented? So, here's how it works: Firstly, for e...

We are pleased to announce the release of ChEMBL_17. This version of the database, prepared on 29th August 2013 contains: 1,519,640 compound records 1,324,941 compounds (of which 1,318,187 have mol files) 12,077,491 activities 734,201 assays 9,356 targets 51,277 documents You can download the data from the ChEMBL FTP site . For more information please read the release notes . Data changes since the last release: Drug mechanism of action For all FDA-approved drugs, information regarding the mechanism of action and associated efficacy targets has been curated from primary sources, such as literature and drug prescribing information. Targets have only been included for a drug if a) the drug is believed to interact directly with the target and b) there is evidence that this interaction contributes towards the efficacy of that drug in the indication(s) for which it is approved. Metal-containing compounds Structures for around 3200 metal-containing compounds have b...

We are pleased to announce the release of ChEMBL_16. This version of the database was prepared on 7th May 2013 and contains: 1,481,473 compound records 1,295,510 compounds (of which 1,292,344 have mol files) 11,420,351 activities 712,836 assays 9,844 targets 50,095 documents 19 activity data sources You can download the data from the ChEMBL ftpsite and do not forget to read the ChEMBL_16 Release Notes Data changes since the last release ChEMBL_16 includes the Millipore Kinase Screening publication ( CHEMBL2218924 ), which is kinase screening panel data set focused on 158 known kinase inhibitors and the OSDD Malaria Screening dataset ( CHEMBL2113921 ), which is a set of anti-malarial compounds and bioactivity data provided by the OSDD Malaria consortium .  In addition to the our regular publication and dataset updates we are now also loading supplementary bioactivity datasets. In this example the original paper from GSK was published in 2010 ( CHEMBL1157114 )...