ChEMBL_16 Released

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) and with the release of ChEMBL_16 we now provide 2 supplementary datasets (CHEMBL2218064 and CHEMBL2094195). You can see the original paper an supplemenatry datasets in screenshot below (this also demonstrates the new document search functionality we have added to the interface):

We are would like grow our supplementary bioactivity datasets, so please get in touch if you have any similar data you would like to deposit in the ChEMBL database. Stefan Senger from GSK, has put together the following slides, which provide more details on the pros and pros of depositing supplementary bioactivity data. (Also thanks Derek Lowe over at In The Pipeline for the following blog post).

Interface changes since the last release:
We have made a number changes to the interface which are listed below:

Document Search - Submit a keyword search against journal articles and datasets loaded into the database
Browse Targets - We have improved the tree browser on protein classification and organism browser targets page
Browse Drugs - Now allows searching on USAN stem and ATC code definitions
Updated FAQ pages - see here
Target Report Card - Now contains a target relation section, providing links between targets sharing protein components. The target report card also includes links to CREDO and TIMBAL databases
Compound Report Card - Includes a link to NCI Resolver service, to retrieve additional synonyms for a compound

In addition to our regular set of downloads (Oracle, MySQL, PostgreSQL) you will also find RDF version on the ChEMBL database. The current version is 16.0 and the files are available to download here. You can expect some minor changes in the RDF between now and the ChEMBL_17 release and these will be represented by increments in the minor version number

The ChEMBL Team

Comments

Improvements in SureChEMBL's chemistry search and adoption of RDKit

Dear SureChEMBL users, If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever. What's New? Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL . This update allows SureChEMBL to leverage our FPSim2 Python package , returning results in approximately one second. The similarity search relies on 256-bit RDKit -calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run. SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab ! For substructure searches, we now also use an RDKit -based solution via SubstructLibrary , which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by

Improved querying for SureChEMBL

Dear SureChEMBL users, Earlier this year we ran a survey to identify what you, the users, would like to see next in SureChEMBL. Thank you for offering your feedback! This gave us the opportunity to have some interesting discussions both internally and externally. While we can't publicly reveal precisely our plans for the coming months (everything will be delivered at the right time), we can at least say that improving the compound structure extraction quality is a priority. Unfortunately, the change won't happen overnight as reprocessing 167 millions patents takes a while. However, the good news is that the new generation of optical chemical structure recognition shows good performance, even for patent images! We hope we can share our results with you soon. So in the meantime, what are we doing? You may have noticed a few changes on the SureChEMBL main page. No more "Beta" flag since we consider the system to be stable enough (it does not mean that you will never

ChEMBL brings drug bioactivity data to the Protein Data Bank in Europe

In the quest to develop new drugs, understanding the 3D structure of molecules is crucial. Resources like the Protein Data Bank in Europe (PDBe) and the Cambridge Structural Database (CSD) provide these 3D blueprints for many biological molecules. However, researchers also need to know how these molecules interact with their biological target – their bioactivity. ChEMBL is a treasure trove of bioactivity data for countless drug-like molecules. It tells us how strongly a molecule binds to a target, how it affects a biological process, and even how it might be metabolized. But here's the catch: while ChEMBL provides extensive information on a molecule's activity and cross references to other data sources, it doesn't always tell us if a 3D structure is available for a specific drug-target complex. This can be a roadblock for researchers who need that structural information to design effective drugs. Therefore, connecting ChEMBL data with resources like PDBe and CSD is essen

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains: 2,431,025 compounds (of which 2,409,270 have mol files) 3,106,257 compound records (non-unique compounds) 20,772,701 activities 1,644,390 assays 15,598 targets 89,892 documents Data can be downloaded from the ChEMBL FTP site: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

ChEMBL 26 Released

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

The ChEMBL-og

Search This Blog