The ChEMBL-og

We're excited to announce a new feature on ChEMBL compound pages: an interactive 3D viewer showing a low-energy, quantum-mechanically informed conformer for each compound, wherever one is available. This is part of a collaboration with the Isayev Lab at Carnegie Mellon University who have developed ChEMBL3D. Until now, ChEMBL compound pages have shown molecules as flat 2D structures. A 2D depiction is great for seeing connectivity, but it says nothing about a molecule's actual shape in three dimensions, and shape is often what determines whether a compound fits a binding pocket, how it interacts with a target, or how its stereochemistry affects potency. With this release, you can rotate, zoom, and explore a real 3D conformer directly on the compound page, view it alongside the familiar 2D structure, and download the coordinates as an SDF file. The 2D and 3D visualization options in ChEMBL for the sample molecu le Imatinib (CHEMBL941),   https://www.ebi.ac.uk/chembl/explore...

Thank you to everyone who has shared feedback with us through our UX studies and conversations with the ChEMBL team. Your input has helped us understand what’s working well, what could be smoother, and where small changes could make a big difference. Based on that feedback, we’ve made a few updates to the ChEMBL web interface that we hope will make browsing, searching, filtering, and exploring data a little easier. We’d love for you to try them out and let us know what you think. Filters that stay with you The filters panel is now sticky, so it stays visible while you scroll through results. This should make it easier to refine searches without having to jump back up the page. We’ve also updated the histogram-style filters so the bars include counts directly inside them, making it easier to scan the available values at a glance. And when a filter section has more options available, there is now a “See all” button so you can expand the full list of facets. Histogram filters before and ...

  The Chemical Biology Resources Team at the European Bioinformatics Institute ( EMBL-EBI ) is looking for a talented Scientist with a flair for data curation to be responsible for the quality of bioactivity and drug discovery data in the ChEMBL database . ChEMBL is a world-leading chemogenomics resource, providing open bioactivity data and associated tools to the scientific community. ChEMBL is widely used through both academia and industry to support drug discovery. You will work in a team-oriented environment, collaborating closely with fellow scientists and technical experts, chemo- and bio-informaticians and software engineers across EMBL-EBI and with our many external partners from the UK and internationally. Applicants may be from anywhere in the world (visa support and relocation allowance); also note that the quoted salary is tax free and so is equivalent to the net salary from another job.   For more information, and to apply, click HERE !     Your role ...

We are looking for a talented scientist with a flair for data curation to be responsible for the quality of chemical and associated data in the ChEBI database . In this role, you will contribute to maintaining the quality and integrity of the ChEBI database and ontology through the curation of chemical structures, coordination of data releases, and collaboration with the global scientific community. If you have a background in chemistry or biochemistry and are passionate about open-access scientific data, we would be delighted to hear from you. Applicants may be from anywhere in the world (visa support and relocation allowance); also note that the quoted salary is tax free and so is equivalent to the net salary from another job. For more information, and to apply, click HERE !   Duties & responsibilities    You will be responsible for the curation of chemical data in the ChEBI database. Reporting to the Chemical Biology Services team leader, the job responsi...

The first ChEMBL User Group Meeting in the modern era took place last month.  A huge thanks to everyone who came along and joined the discussions, as well as to the Chemical Biology Services team and the Training team for making everything run smoothly.  The overriding goal of the meeting was to build closer links with the ChEMBL and SureChEMBL community, as well as to get feedback and suggestions on our services.   From our side it was a great success - we have pages and pages of notes from the meeting, and the conference feedback we received was also very positive. Many presenters were able to share slides and make available the recording; these are now available on the conference page .  Given that the meeting went well, we plan to run it again. But perhaps not until 2028 - what do you think?

    This image was generated using AI.   Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday , and Friday in early June.   A typical Friday in Emma’s week     Fridays are usually meeting-free by design. This allows unbroken time to work deeply on tasks. Such tasks include focused curation, enhancements, or investigation into data quirks or errors. Occasionally, we’re also involved in training, data analysis, or drafting publications. On several recent Fridays, biological curators worked alongside other team members on our recent bioassay annotation paper , particularly in the generation of the gold-standard training set. Our biological curation role also extends to the annotation of the comprehensive drug data that can be found in ChEMBL. This means that we gain an insight into emerging modalities making their way through the clinical pipeline. To capture these entit...

    This image was generated using AI.   Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday , and Friday in early June.   A not-so-typical Wednesday & Thursday in Emma’s week The EMBL-EBI offers flexible working and part-time roles, this is part of what makes the working environment so inclusive. My part-time role (4 days/week) means that Wednesdays are usually a non-working day. However, a very special event brought me to the office on Wednesday 10th and Thursday 11th June. ChEMBL held our 2nd User Group Meeting where we welcomed over 60 delegates to our beautiful campus for two days of presentations, case studies, workshops, and networking. It’s rare that we get an opportunity for such close engagement with our community of database depositors and users in a single session, and the event provided an insight into the value of ChEMBL to the Medicinal Chemistry and wider co...

This image was generated by AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday and Friday during the course of a week in early June.   A typical Wednesday in Sally’s week Since we had a special event this Wednesday on 10th June (see Emma’s next blog article ), I’ll talk about the routine work I completed on 17th June instead. UniProt recently published a new release in which roughly 57 million protein entries were retired. Because ChEMBL maps protein targets to UniProt accessions, my task today is to replace obsolete accessions with active ones wherever possible. This isn’t as straightforward as it may sound, though. I frequently have to go back to the source publication to find more information on a given target. For example, I might need to confirm the exact strain that was studied, compare protein lengths or molecular mass, or check if the authors themselves provided a protein accession...

This image was generated using AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday and Friday during the course of a week in early June. A typical Tuesday in Sally’s week First thing in the morning of Tuesday 9th June, I dedicate some time replying to Helpdesk enquiries and catching up on any new GitHub data issues . One user reports an assay that has been assigned to the wrong target in ChEMBL. I briefly double check the source document to verify the information and thank the user for reporting the error. Luckily, it’s an error that’s easy to fix, so I write an SQL update statement to correct the target in our internal production database. Then I run a brief check to see if the same issue affected any other assays in ChEMBL. Updating this information ensures that the next ChEMBL release will incorporate the fix. It’s also a good reminder that user feedback plays an important role in helping u...

  This image was generated using AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to during the course of a week in early June. There are two biological curators in the ChEMBL team. Together, we'll revisit that week one day at a time, in a new blog post each day. Sally will highlight some of the routine tasks that we might undertake on a Monday , Tuesday or Wednesday , whilst Emma will describe some of the less typical activities that we might be involved in during the second half of the week on a Thursday and Friday . Our days usually begin around 8.30-9am and finish at 5-5.30pm. Two or three of these days are in-person, with some flexibility. The EMBL-EBI offices are part of the Wellcome Genome Campus, a hub of scientific, and particularly genomics, institutes. Wetlands surround the carefully crafted and biodiverse grounds - meaning a lunchtime walk is always tempting! A typical Monday in Sally’s week It’s Monday 8th June and I star...

Slides and recordings from the recent ChEMBL UGM are starting to appear on the meeting website. Here I want to draw attention to the presentation by Nicolas Bosc and myself on " SureChEMBL: Your next source of research data ". Ever since my NextMove Software days, I've been aware of the large amount of scientific data available in patents. This includes everything from large sets of chemical analogs, to bioactivity values, reactions, and NMR spectra. US patents in particular are a rich source of data as they are (a) born digital, and (b) freely available, and thus automated tools to extract relevant data can generate substantial high quality datasets. For example, here's a graph I did back in 2017 to illustrate a NextMove Software blog post entitled "Are more bioactivities available from patents than from the academic literature?". This compared the data deposited from papers into ChEMBL and that extractable by LeadMine from patents (see the talk linked fr...

The Chemical Biology Services team invites applications for a 3-year ARISE2 Postdoctoral Fellowship – a unique postdoctoral opportunity that combines advanced research training with hands-on experience in developing innovative technologies and methods to enhance scientific services. Why apply? Make an Impact: Collaborate on high-impact projects that will directly shape and improve the scientific services we provide. Tailored to You: Each fellowship project is developed in collaboration with the fellow and the host team – possibly even involving an industry partner – to ensure a project that combines your ideas with the vision of of the host. Prepare for the Future: The ARISE2 Fellowship is designed to prepare fellows for dynamic careers within research infrastructures, providing both technical depth and professional development. If this sounds interesting, please get in touch by the end of August at oboyle@ebi.ac.uk with your CV. Note that we recruit worldwide. Here is...

We are looking for a highly motivated Computational Biologist / Bioinformatician (*) to join the Chemical Biology Resources team at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus near Cambridge, as part of the Wellcome Trust funded LIGMAP project, a multi-disciplinary collaboration between University College London and EMBL-EBI. LIGMAP is an ambitious multiyear project, led by University College London, to identify the endogenous ligands of the many proteins of unknown function in the proteome using AI-based methods as well as classical machine learning. You will work closely with the PDBe team at EMBL-EBI, as well as leading researchers in structural biology and machine learning at University College London, to deliver the goals of the project. You will develop descriptors to characterise the binding site of proteins in terms of their ability to recognise ligands, and use these to assess druggability of protein binding sites.   This positi...

ChEMBL 37 arrives with nearly three million compounds, a new modality field for capturing targeted protein degraders, and a wave of data quality improvements.    A new field for targeted protein degradation Around 29,000 bioactivity data points have been annotated with     ACTIVITIES.MODALITY  = “Targeted Protein Degradation” , including around 3,000 legacy bioactivities from approximately 1,200 remapped assays. This marks ChEMBL’s first systematic effort to flag TPD data across the database.        Extensive update of literature data Scientific literature remains the backbone of ChEMBL, and ChEMBL 37 brings one of the more substantial literature updates in recent releases. Compared to ChEMBL 36, the literature source gained approximately 79,000 new assays, 270,000 new bioactivity data points, and 52,000 new compound records — pushing the total literature-derived activity count past 9.55 million. Twelve new c...