Annotation of ChEMBL with compound availability data

We are starting to plan a few things, and one of these is to provide links through to the sources of physically available compounds for ChEMBL. To help us, here's a few questions - I tried to set up an online poll, but lost the will to live with all the spam on polls that is out there.

Here are the questions:

Is integration of available compounds in ChEMBL a good idea?
Should we integrate available compounds via current informatics resources (e.g. ZINC, ChemSpider)?
Should we set up a small set of available compounds from actual suppliers (e.g. NCGC, MolPort, Prestwick, ChemDiv, Tocris, etc. etc.). If so what suppliers should we use?

If you want to contribute, free to mail if you have any specific ideas, or can help us out on this.

Comments

eMolecules said…

You might consider eMolecules, which lists only in-stock compounds. Most other data collections list historic and virtual compounds, leading to success rates of actually getting the compounds below 50%. Maintaining your own collection of supplier catalogs is very time consuming and it is hard to keep them up to date.
Our data content is publicly available.

klaus@emolecules.com

22 June 2011 at 16:13

Bio to Chem said…

One way or the other most suppliers are already connected via the PubChem and ChemSpider outlinks. I would not have thought it worth your efforts (vs other good stuff) to add these directly. JFTR its easy to make the intersects in PubChem (e.g. a ChEMBL AID > CIDs > history > AND source MolPort OR ZINC OR... etc)

24 June 2011 at 13:15

Imants said…

As Chris mentions, you already have a link to Molport and other databases via PubChem. A more direct integration with an ordering platform has some additional benefits, however. For example, at Molport we are thinking of ways how to give partner applications a quick way to check which compounds are available today, at the moment the user views the compound. Here is my blog post about it: http://blog.molport.com/2011/06/quick-way-to-programmatically-check.html

I agree with Dr. Gubernator - it is huge task to keep supplier catalogs updated.

29 June 2011 at 21:53

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