I am pleased to share our work “Characterising AlphaFold 3’s ability to predict T cell antigen specificity” (www.biorxiv.org/content/10.6...)!

Characterising AlphaFold 3’s ability to predict T cell antigen specificity

T cells are a key part of the adaptive immune system. Using their surface-bound T cell antigen receptors (TCRs), these cells scan peptides and other antigens presented to them by major histocompatibil...

biorxiv.org

Today, we're announcing SAbDab2! In brief: - clean, pre-processed antibody structure data for ML with standardised train/test splits - massive improvements in structure organisation and annotation consistency - support for VNARs and antibody construct annotation - more structures than ever before

Following some routine maintenance to our web servers, we are experiencing some delays in bringing OPIG's web services back up. We apologise for this and will post an update here when we have resolved the issue

Please be aware that OPIG's web apps will be down for maintenance from 09:00 UTC on Tuesday 28th April 2026 and unavailable for a period of approximately one hour. Apologies for any inconvenience and for the short notice of this downtime.

What would you tell your younger self? For International Day of Women and Girls in Science, Professor Charlotte Deane shares her advice: worry a little bit less, and just go and do what you really enjoy doing. #IDWGS

We are excited that Charlotte Deane will be speaking at NextGen Biomed 2026! NextGen Biomed runs from 24-25 March 2026 at the QEII Centre, London, UK. Pharma and biotech R&D leaders will come together to explore the future of biologics and immunotherapy hubs.la/Q03-WVg40 #NGB2026 #OGNextGenBiomed

We are delighted to once again support the UNIQ+ programme and offer two projects in OPIG this summer! UNIQ+ is a paid summer research internship and is open to UK undergraduates from under-represented and disadvantaged backgrounds 📆 Applications close 18 Feb 👉 Apply: www.ox.ac.uk/admissions/g...

We're also happy to share that "Inferring residue level hydrogen deuterium exchange with ReX" by Oliver Crook, Charlotte Deane, and co-authors Nathan Gittens & Chun-wa Chung from GSK, was published in Communications Chemistry in the tail end of 2025. www.nature.com/articles/s42...

Inferring residue level hydrogen deuterium exchange with ReX - Communications Chemistry

Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) is a powerful method to study protein conformational dynamics, but peptide-level measurements obscure residue-level detail. The authors present R...

nature.com

Next, we are happy to announce that our pandemic preparedness orthopoxvirus antibody database “Pox-AbDab” has now been published in Frontiers in Immunology. First data update to come later in January! Paper: doi.org/10.3389/fimm... Database: opig.stats.ox.ac.uk/webapps/poxa...

Frontiers | Pox-AbDab: the orthopoxvirus antibody database

In August 2024, the World Health Organization declared the mpox orthopoxvirus to be a Public Health Emergency of International Concern for the second time in...

doi.org

A happy new year from all at OPIG! We start the year with an article in Expert Opinion on Drug Discovery by Charlotte Deane and co-founders at DaltonTx. Here, they share a vision of integrating computation into drug discovery for maximum added value & efficiency www.tandfonline.com/doi/full/10....

From algorithms to systems: integrating computation into drug discovery

Despite remarkable advances in computational methods, pre-clinical drug discovery continues to grapple with rising timelines and costs. Software, data, and automation are more powerful than ever, a...

tandfonline.com

I'm really pleased that our collaboration with Shira Sagie, Tomer Babu and Yardena Samuels has been published in Cell Reports Medicine. This has been a really fun and productive collaboration as well as an incredible learning process. www.cell.com/cell-reports...

Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation

Sagie et al. identify a KRAS.G12V-specific TCR and show that lymphodepleting chemotherapy enhances antigen presentation via immunoproteasome activation and HLA-I upregulation. Together, these changes ...

cell.com

My first full contribution from my time in @opig.stats.ox.ac.uk is now out! Together with @fspoendlin.bsky.social (and with contributions from King Ifashe), we created FlAbDab and FTCRDab: two large-scale, open molecular dynamics datasets to study flexibility in immune receptors.

Excited to share our new review on deep learning for structure-based drug design! 🎉 pubs.rsc.org/en/content/a... Authors: @lucyvost.bsky.social*, Yael Ziv*, Charlotte Deane

STCRpy, an easy-to-use python package for T-cell receptor structures has just been published in Bioinformatics! Big thanks to @mraybould.bsky.social and Charlotte Deane for their support, and to @opig.stats.ox.ac.uk for being an amazing collaborative group! Paper: doi.org/10.1093/bioi...

STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation

AbstractSummary. Computational methods to guide early-stage TCR drug discovery and TCR repertoire informatics currently under-utilize solved and predicted

doi.org

We won the Boltz Hackathon Challenge improving computational efficiency! Big thanks to Boltz team and @merckgroup.bsky.social for the event and very proud of our prototype Boltz Flow Matching model. Huge thanks to Niklas Abraham and Aaron Schöne for being excellent collaborators! ms.spr.ly/6043tBeAL

Recently, Prof. Charlotte Deane participated in a discussion about AI as part of the Bradford Science Festival. Read some of her (and the other participants') thoughts here: blog.scienceandmediamuseum.org.uk/how-britain-...

How Britain can harness the AI revolution - National Science and Media Museum blog

Roger Highfield, Science Director, reports on an AI discussion at the Bradford Science Festival.

blog.scienceandmediamuseum.org.uk

📜 New preprint! Syndirella is a pipeline for proposing synthesis-directed elaborations for fragment-inspired designs with explicit routes and poses! Preprint: chemrxiv.org/engage/chemr... Code: github.com/oxpig/syndir...

Syndirella: Synthesis-directed fragment elaboration enables extensive binding site exploration beyond catalog compounds

Fragment screens provide an information-rich starting point for designing derivative compounds that recapitulate key protein-ligand interactions in structure-based drug discovery. Maximizing the compo...

chemrxiv.org

Please be aware that OPIG's website and web apps will be down for maintenance from 09:30 UTC on Tuesday 14th October 2025, and will be unavailable for approximately one hour. Apologies for any inconvenience and for the short notice of this downtime.

AIR Street Capital's "State of AI" 2025 Report references Nicholas Runcie, Charlotte Deane, and Fergus Imrie's work on Assessing the Chemical Intelligence of Large Language Models. Read the whole report here: stateof.ai And our preprint here: lnkd.in/gbuNXR93

State of AI Report 2025

The State of AI Report analyses the most interesting developments in AI. Read and download here.

stateof.ai

🚨 We’re hiring! The OPIG group is looking for multiple postdocs to join OpenBind, an open science initiative generating foundational structural biology data to power the next era of AI/ML for drug discovery. opig.stats.ox.ac.uk openbind.uk

New episode of Agents of Tech!🚨“AI is going to completely change the way we ask questions" We were thrilled to be joined at ISMB/ECCB by Prof. Charlotte Deane to discuss the changing role of AI in science and why humans will always be essential #ai #podcast @iscb.bsky.social

AI can’t work without data. OpenBind could spark the next revolution in AI drug discovery, building the datasets we need to predict how small molecules bind to proteins. Full episode out now! #AI #OpenBind #AlphaFold #Biotech #ArtificialIntelligence

“We are the third best country in the world at AI… that’s incredible. Start there.” Live from ISMB/ECCB, Professor Charlotte Deane reflects on the 'AI race' - is it really about competition? And does the UK have a true strategic advantage? @iscb.bsky.social #podcast #ai #academicsky #research

🚨Our August issue is now live and includes research on antibody-antigen binding, molecular screening for zeolite synthesis, psychological experiments with LLMs, and much more! www.nature.com/natcomputsci...

Our paper on generalizable antibody-antigen binding affinity prediction has been featured on the cover of the August Issue of @natcomputsci.nature.com! 📔🎉

Nature Computational Science@natcomputsci.nature.com · 12mo ago

🚨Our August issue is now live and includes research on antibody-antigen binding, molecular screening for zeolite synthesis, psychological experiments with LLMs, and much more! www.nature.com/natcomputsci...

Our first pandemic preparedness database, Pox-AbDab, is now available! We present sequence, structural & functional data on antibodies and nanobodies that bind/neutralise orthopoxviruses: DB: opig.stats.ox.ac.uk/webapps/poxa... Preprint: doi.org/10.1101/2025... Work led by Henriette Capel

Our preprint, LICHEN: Light-chain Immunoglobulin sequence generation Conditioned on the Heavy chain and Experimental Needs, is now on bioRxiv. LICHEN is a machine learning tool to generate an appropriate light sequence for a given heavy sequence. www.biorxiv.org/content/10.1...

LICHEN: Light-chain Immunoglobulin sequence generation Conditioned on the Heavy chain and Experimental Needs

In developing therapeutic antibodies, the heavy chain is often prioritised due to its higher variability and its central role in antigen binding. An appropriate pairing of the light sequence is howeve...

biorxiv.org

🛠️ Web apps are back! We completed our scheduled maintenance this morning. If you notice any issues, please let us know at opig<~at~>stats.ox.ac.uk!

🛠️ Scheduled maintenance Please be aware that OPIG's website, including our web apps, will be down for routine maintenance at 10:00 UTC on Monday 11th August 2025 for a period of approximately one hour. Apologies for any inconvenience.

Our paper "Transformers trained on proteins can learn to attend to Euclidean distance" is now published in @tmlrorg.bsky.social @tmlr-pub.bsky.social openreview.net/forum?id=mU5...