Fergus Imrie

🚀 LLMs can now do chemistry! Our new preprint shows that state-of-the-art reasoning models can now perform advanced chemical reasoning tasks, without any assistance from external tools. Here’s what o3-mini can already do👇 (1/🧵)

MolSnapper: Conditioning Diffusion for Structure-Based Drug Design Generative models have emerged as potentially powerful methods for molecular design, yet challenges persist in generating molecules that effectively bind to the intended target. The ability to control the design process and incorporate prior knowledge would be highly beneficial for better tailoring molecules to fit specific binding sites. In this paper, we introduce MolSnapper, a novel tool that is able to condition diffusion models for structure-based drug design by seamlessly integrating expert knowledge in the form of 3D pharmacophores. We demonstrate through comprehensive testing on both the CrossDocked and Binding MOAD data sets that our method generates molecules better tailored to fit a given binding site, achieving high structural and chemical similarity to the original molecules. Additionally, MolSnapper yields approximately twice as many valid molecules as alternative methods.

MolSnapper has been published in @pubs.acs.org Journal of Chemical Information and Modeling!

MolSnapper integrates expert knowledge into diffusion models for structure-based drug design using conditioning

Congratulations Yael Ziv, Fergus Imrie, Brian Marsden, and Charlotte Deane

shorturl.at/8PeWT

Starting in October, great for final year PhD students or someone who has recently received their doctorate.

Deadline to apply: 30th April, midday UK time

Job advert: shorturl.at/3l47e
Further details of the fellowship and specific project: shorturl.at/AffOb

3-year postdoc opportunity as part of the Novo Nordisk - Oxford Fellowship programme!

Develop machine learning approaches for drug discovery with me, Charlotte Deane (Oxford), and Christos Nicolaou (Novo Nordisk).

1 week left to apply! Details in next post

We're recruiting a 3-year postdoc for the Novo Nordisk - Oxford Fellowship programme!

Develop machine learning approaches for fragment library design and experimental optimisation

With @fergusimrie.bsky.social and Charlotte Deane

Job advert: shorturl.at/3l47e
Further details: shorturl.at/u4UkK

This International Women's Day, we proudly recognise the amazing women in OPIG and all their exceptional work and achievements

Amazing program. I'm very excited to be a co-supervisor for a UNIQ+ project on Nanobody Language Modelling based in @oxfordstatistics.bsky.social

If you're eligible and think you might want to pursue post-grad study, UNIQ+ is a great intro to research and well-funded (paid + free accommodation)

🔥 Molecule networks 🔥 New cheminformatics data visualisation:

📊 Rapid interpretation of SAR
🔊 Find molecules in the noise
❌ No more lists of molecules

My new favourite visualisation method!

🚀 Read how I visualise Free Wilson analysis here

www.blopig.com/blog/2025/01...

🚨 PhD openings

Fantastic opportunity to join @ox.ac.uk for a PhD as part of the new ILESLA programme

Research possible across 5 broad themes including machine learning and drug discovery. Opportunities to work with me, @opig.stats.ox.ac.uk and many others

Deadline: Jan 31st, 12pm (midday) UK time