Blogging from the ACS

I'm at the ACS in San Diego this week, there are three of the ChEMBLites here - two talks down, one to go. It's been a really great meeting, really excellent. I've even managed to sort of stay on UK time, so waking up at about 2am, and then having a good session on the computer before talks start at 8am. My only moan has been that on the computational side, there are too many interesting parallel sessions, and it's difficult to choose where to go. Anyway, I've spent some time with old and new friends, and feel really upbeat about the way that chemoinformatics is impacting our understanding of biology, and how progress is being made in how to design compounds that modulate biological systems. I sense that the availability of large-scale data and large-scale computing are really feeding off each other and allowing things to be developed that could only be imagined a few years ago.

And in a great advance for mankind, internet is free at the conference; seriously well done ACS for sorting this out - I'm fed up of paying serious cash for internet access at conferences.

Blogging really seems to have taken off this year - or at least I'm starting to track live blogging more than I did - Rajarshi Guha of NCTT has been a superstar - here's his twitter feed. A must follow account for those in the field.

Also great has been Carmen Drahl of the ACS itself - here's her twitter feed. Of particular note is the live-blogging she did on first time med. chem. disclosures. Great service - here's the link to the CEN hosted blog. I think there is a great opportunity here to help the world - crowd sourcing and immediately distributing key facts, Carmen has naturally focussed on the chemical structure aspects; but imagine if there were more like-minded people who captured this sort of really valuable data and tweeted or blogged as a community, in a way that others not able to be there could react to the data, analyse it and integrate in their research. If done right, and more importantly could be integrated into a living public and fully Open resource. If the world was even more perfect, the presenters would immediately post their slides online, with semantically marked up assays and InChIs of all the compounds.... hey, you can tell I'm in California!

The ACS tattoo above is pretty cool; maybe if you ask me nicely when we meet, I can show you mine.

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New SureChEMBL announcement

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f

Legacy SureChEMBL retirement

Dear SureChEMBL users, About six months ago, we introduced the new version of SureChEMBL . It brought significant improvements in terms of performance and stability, and it also allows us to implement new functionalities. After the survey at the beginning of the year, we prioritised what should be delivered first. You should see the materialisation of our work in the coming months. As originally announced when the new SureChEMBL was introduced, the plan was to shut down the old system permanently to focus all our resources on the new SureChEMBL. This time has come, so expect www.surechembl-legacy.org to be unreachable in the coming days with no turning back! Consequently, and in parallel, the new SureChEMBL will lose its Beta status, and we will stop referring to it as the new version. This does not mean we are reducing our efforts to improve our system; on the contrary, this removes a distraction! If you have any feedback, you can contact us directly at surechembl-help@ebi.ac.uk . W

ChEMBL & SureChEMBL anniversary symposium

In 2024 we celebrate the 15th anniversary of the first public release of the ChEMBL database as well as the 10th anniversary of SureChEMBL. To recognise this important landmark we are organising a two-day symposium to celebrate the work achieved by ChEMBL and SureChEMBL, and look forward to its future. Save the date for the ChEMBL 15 Year Symposium October 1-2, 2024 Day one will consist of four workshops, a basic ChEMBL drug design workshop; an advanced ChEMBL workshop (EUbOPEN community workshop); a ChEMBL data deposition workshop; and a SureChEMBL workshop. Day two will consist of a series of talks from invited speakers, a few poster flash talks, a local nature walk, as well as celebratory cake. During the breaks, the poster session will be a great opportunity to catch up with other users and collaborators of the ChEMBL resources and chat to colleagues, co-workers and others to find out more about how the database is being used. Lunch and refreshments will be pro

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.

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

The ChEMBL-og

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