ChEMBL 20 coming soon...

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 viewed on the interface and the full data set will be included in the database downloads.
Cell Report Cards - we will now provide ChEMBL IDs and Report Card pages for cells and cell-lines, as well as a keyword search facility. This will enable users to quickly identify all assays that have been performed in a particular cell-line and will also provide cross references to other resources such as the LINCS project.
HRAC/FRAC/IRAC classification - for known herbicides, fungicides and insecticides, we provide their classification according to HRAC/FRAC/IRAC. This gives an indication of the mechanism of action of each compound. The classification can be found on the compound report card for these crop protection chemicals.
New bioactivity data - in addition to the usual updates of bioactivity data from scientific literature and PubChem BioAssay we have 12 new sets of screening results from the MMV Malaria Box and an extensive set of in vitro DMPK and physiochemical property data for more than 5,700 publicly disclosed drugs and compounds deposited by AstraZeneca.
There will be some schema changes to incorporate these new features, but these will be additions and are unlikely to break existing code.

Watch this space!

The ChEMBL Team

Comments

Samo said…

Will you make the SMARTS patterns freely available?

7 January 2015 at 08:46

christian_l said…

How soon after that are you planning to release myChEMBL 20?

I'm also very interested in the SMARTS patterns!

7 January 2015 at 18:28

Anna said…

Yes, the SMARTS will be available in the database downloads.

20 January 2015 at 07:52

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