ChEMBL_17 Released

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 been removed from the database (though the bioactivity and other information for these compounds is retained). For more information, please see the previous blog posts: http://chembl.blogspot.co.uk/2013/08/removal-of-metal-containing-compounds.html

New data sets

Several new deposited/extracted data sets have also been included in the latest release: two deposited data sets from GlaxoSmithKine for Ghrelin receptor agonists and Motilin receptor agonists, a data set of the results of screening the MMV Malaria Box compound collection for activity against Schistosoma mansoni, two data sets screening the GSK PKIS compound collection for inhibition of luciferase activity, and finally pathology data from the Open TG-GATES project.

Interface changes since the last release:

Browse Drug Targets tab

A new tab has been created to show the new mechanism of action information for FDA approved drugs together with the references from which the information was obtained, and links to the relevant drug/target report card pages.

Document Report Card

A new table has been added to the document report card, showing other ChEMBL documents that are related to the current document. Pair-wise document similarity is assessed by two components. The first component is defined by whether a document cites or is referenced by the other. The second component is defined by the amount of overlap between the compounds and biological targets reported in the two respective documents. This overlap is quantified by the Tanimoto coefficient. Documents with the highest Tanimoto similarity scores to the query document are listed in this section. For example, the following page shows 5 additional ChEMBL documents that are deemed similar to the paper currently being viewed.

Database changes since the last release:

A number of new tables have been added to store the drug mechanism of action information (please see release notes and schema documentation for full details). In addition, a number of minor changes have been made to existing tables:

The PROTEIN_FAMILY_CLASSIFICATION table has been deprecated and replaced by a new hierarchical version: PROTEIN_CLASSIFICATION.

The MOLREGNO field has been removed from the ATC_CLASSIFICATION table and moved to a new mapping table: MOLECULE_ATC_CLASSIFICATION.

The MOLFORMULA field has been moved from the COMPOUND_STRUCTURES table to the COMPOUND_PROPERTIES table (and renamed).

The ChEMBL Team

Comments

Egon Willighagen said…

Can you make available the list CHEMBL ids of those 3200 metal-containing compounds?

17 September 2013 at 08:18

Here's a nice Christmas gift - ChEMBL 35 is out!

Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35! This fresh release comes with a wealth of new data sets and some new data sources as well. Examples include a total of 14 datasets deposited by by the ASAP ( AI-driven Structure-enabled Antiviral Platform) project, a new NTD data se t by Aberystwyth University on anti-schistosome activity, nine new chemical probe data sets, and seven new data sets for the Chemogenomic library of the EUbOPEN project. We also inlcuded a few new fields that do impr ove the provenance and FAIRness of the data we host in ChEMBL: 1) A CONTACT field has been added to the DOCs table which should contain a contact profile of someone willing to be contacted about details of the dataset (ideally an ORCID ID; up to 3 contacts can be provided). 2) In an effort to provide more detailed information about the source of a deposited dat...

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...

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 ...

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...

The ChEMBL-og

Search This Blog