iiinova — where your digital self keeps evolving

Dr Javier Sánchez Utgés @javierutges.bsky.social · 02/10/2026

Ah, that is great. Looking forward to catching up there!

Dr Javier Sánchez Utgés @javierutges.bsky.social · 01/10/2026

Are you working on the field of #Structural #Bioinformatics and have not registered yet? What are you waiting for? Join me and the community in attending this excellent meeting in beatiful and history-rich #Rome! I am so excited for this and cannot wait to see you all there!

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Reposted by Dr Javier Sánchez Utgés

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24/09/2026

AlphaFold Database is expanding into pandemic preparedness. Together with NVIDIA, DeepMind, EBI et al. we exhaustively predicted ~1.7 million homo- & heterodimers across 2,812 viral proteomes, resulting in 8,028 high-confidence predictions. 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

6/6 🔑 Overall, our work helps clarify what contrastive pocket-ligand models learn, where they work well & where they can improve. We hope it also provides a useful framework for studying related methods such as DrugHash, BindCLIP & ConGLUDe. Thanks to everyone involved! 🙌

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

5/6 🔹 For novel targets, DrugCLIP recovers the correct bound ligand within the top 1% of ~50,000 compounds in 55-75% of cases. Performance drops in more realistic scenarios, driven by sidechain orientation and, for predicted pockets, differences in pocket residue selection.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

4/6 🔹 Ligand embeddings capture a more pocket-aware notion of chemical similarity, rather than simply reproducing fingerprint similarity. After rigorous de-leakage, we also find that DrugCLIP generalises to both proteins AND chemistry unseen during training. 🧬 💊

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

3/6 🔹 DrugCLIP sets a new state of the art for pocket similarity search – despite not being trained for this task – while running >100× faster than existing structural descriptors. Its pocket embeddings strongly track structural similarity and are robust across conformations.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

2/6 💊 What does DrugCLIP actually learn? DrugCLIP represents protein pockets and small molecules as vectors in a shared embedding space for virtual screening. We took a deep dive into its latent space to understand what information these abstract representations actually capture. 🔎

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 21/09/2026

🧵 1/6 🚀 Happy to share our latest preprint, now accessible on @biorxivpreprint.bsky.social: “Interrogating contrastive learning embeddings for structure-based virtual screening: a case study on DrugCLIP” My first paper of the postdoc era, so definitely a special one! 📜 doi.org/10.64898/202...

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Reposted by Dr Javier Sánchez Utgés

bioRxivpreprint @biorxivpreprint.bsky.social · 19/09/2026

Interrogating contrastive learning embeddings for structure-based virtual screening: a case study on DrugCLIP www.biorxiv.org/content/10.64898/20…

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

I cannot wait for #ISMB + #ECCB in #Copenhagen next year. I hope to see many of you there! 🇩🇰

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

Events like ECCB are a great reminder of how valuable it is to bring the computational biology community together to exchange ideas, share new research, and build collaborations!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

A huge thank you to the @sib.swiss for organising such an enjoyable and stimulating conference, and to #ELIXIR for its generous support. Thanks also to all the volunteers, speakers, session chairs, and everyone else involved behind the scenes!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

#1 📜: tinyurl.com/Utges-LYGISIS #2 📜: tinyurl.com/Utges-LBS #3 📜: tinyurl.com/Utges-FRAGSYS #4 📜: tinyurl.com/Utges-SACK1G

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

I presented my #PhD work with @gjbarton.bsky.social at the University of Dundee, on the #LIGYSIS web server (#1) and its diverse applications in #ligand site #prediction performance evaluation (#2), #functional #site characterisation (#3) and prioritisation (#4), as well as further ongoing on this!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

- “A linear interpretable model for Drug Target Prediction” by Santiago Ferreyra

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

Here are some of my favourite talks: - “Stoic: Fast and accurate protein stoichiometry prediction” by Daniil Litvinov - “Efficient sampling of large-scale transition pathways and intermediate conformations in sub-mesoscopic protein complexes” by Domenico Scaramozzino

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

We had three days of interesting #talks, fascinating #keynotes, and many excellent #posters from PhD students and postdocs alike. We also had a great time at the conference #party and enjoying evening drinks by the lake. Oh, yes - and we also had plenty of delicious cheese and meat #fondue! 🫕 🧀

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

#ECCB was the first international conference I attended, back in 2022 in #Sitges, close to home in #Barcelona. Great to reflect on how far I - and many of my peers - have come over the past four years. Many of us were PhD students then and are now postdocs, or transitioned into industry the field!

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Reposted by Dr Javier Sánchez Utgés

Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026

The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions

career5.successfactors.eu

Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/09/2026

Earlier this month, I attended the 25th European Conference on Computational Biology (ECCB) @eccb-europe.bsky.social in beautiful #Geneva, #Switzerland! 🇨🇭

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 30/07/2026

I just submitted an abstract for this amazing #ELIXIR 3D-BioInfo Annual General Meeting | #ISCB #3DSig taking place in beautiful #Rome later on this year in November! Talk abstract submissions deadline is tomorrow, 31 July. Find all the details here: www.iscb.org/3dbioinfo202...! See you in Rome!

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Reposted by Dr Javier Sánchez Utgés

Claudia Alvarez Carreño @claudiaalcar.bsky.social · 09/01/2026

Thrilled to introduce TEDLH, a library of profile HMMs built from TED’s structure-derived domain annotations of the AFDB. Explore 765K HMMs capturing CATH superfamily diversity. www.biorxiv.org/content/10.6...

Construction of TEDLH from TED domain annotations.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 03/02/2026

A couple of quick notes: ✅ All funds go directly to CRUK ✅ If you select 'Gift Aid', an extra 25% is added at no extra cost 🎁

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 03/02/2026

To everyone who donated, shared, commented, or encouraged me along the way - thank you! You made this more meaningful than I can put into words. 💛🙏 My page is still open, so #donations are still welcome if you would like to push a little further: fundraise.cancerresearchuk.org/page/javiers... 🔗

fundraise.cancerresearchuk.org

Javier's Giving Page

Hello there, and welcome, everyone! Thanks for visiting my fundraising page. I am doing the ‘100 Push-Ups a Day’ challenge to help raise money for Cancer Research UK. As the name indicates, I will be ...

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 03/02/2026

And thanks to your #incredible #support, the #fundraising result is honestly beyond what I expected: 🏆 Total raised: £940.00 + £207.52 Gift Aid 📈 Ranked #75 (3%) out of 2,500 challengers (with at least one donation) - or 8,500 (1%) total participants. Great job, everyone!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 03/02/2026

Hi, everyone. I did it! ✅ 💪 #Challenge complete: 31 days of 100 push-ups a day - finished! 🔥 I started this as a small personal commitment with a big purpose: to support @cancerresearchuk.org and help fund vital work in #cancer #research. 🎗️

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/01/2026

If you would like to learn more, follow my progress, or donate in just a few clicks, here is my CRUK giving page: 👉 tinyurl.com/JSU-CRUK A couple of quick notes: ✅ All funds go directly to #CRUK ✅ If you select 'Gift Aid', an extra 25% is added at no extra cost to you (if eligible). 🎁

tinyurl.com

Javier's Giving Page

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/01/2026

Last year, 90K+ people took on #CRUK challenges and raised over £17M to support #cancer research - an incredible #collective #effort. 🙌 Now, I am aiming to add my small contribution to this momentum. So far, I have raised £300 and would love to make an even bigger impact. Every donation helps! 💛

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/01/2026

Hi everyone! 👋 I wanted to share a small personal #challenge with a big #purpose: for the past 15 days I have been doing 100 push-ups a day, and I am committed to keep going for the next 16 days too. 💪 🔥 This is a @cruk-mi.bsky.social initiative to help fund vital work in #cancer #research. 🎗️

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🎙️ Thanks to everyone that helped on this project: Nicola Wood, Thomas Macartney, MRC PPU Reagents and Services, Dundee Uni DTS, @bartongrp.bsky.social, @jalview.bsky.social team, James Abbot and also @martinsteinegger.bsky.social and his team for the excellent #ColabFold implementation!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🔑 Our findings demonstrate the #utility of our #computational #methods to uncover #functional #residues on proteins based on fragment-binding sites. 📜 PAPER: doi.org/10.1098/rsob... 🔗 FRAGSYS: doi.org/10.1038/s420...

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

✨ Additionally, we identified a #sequence #motif highly #conserved in both sequence and structure across the #FAM83 family that likely plays a #regulatory role in the #protein's #function and potentially the pathogenesis of #PPK!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🧫 Beautiful #experimental work led by Diane Lee uncovered two mutations on #FAM83G that abolish SACK1G-CK1α interaction, thus disrupting #WNT signalling, in a similar manner as previously reported #PPK pathogenic variants.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

💻 Using the #fragment #screening analysis from our #FRAGSYS pipeline, combined with high quality #Google #Deepmind's #AlphaFold #Multimer (ColabFold) models of the #SACK1G dimer, we identified and #prioritised 13 #residues in a binding site of interest as likely #functionally #relevant.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🚀 In this study, @gjbarton.bsky.social and I collaborated with the group of Gopal #Sapkota at the @mrcppu.bsky.social at the #SLS of the University of Dundee to shed some light into the loss of interaction between #SACK1G and #CK1α, which underlies the pathogenesis of Palmoplantar Keratoderma (PPK).

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/01/2026

🎉 Happy #new #year to everyone! 📢 No better way to kickstart 2026 than by sharing our latest work, now available on #Open #Biology by @royalsociety.org. The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α".

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🔮 I cannot wait to see what everyone will have accomplished by this time next year. Hope to see many of you again in either #Washington or #Basel!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

I also truly appreciated the chance to meet my future colleagues @nbordin.bsky.social, David Miller, Vaishali Waman, @judewells.bsky.social and Ian Sillitoe. I am thrilled to be joining your team soon!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

A special shout-out as well to friends from @charlesuni.cuni.cz at beautiful Prague — @davhox.bsky.social, Vít Škrhák, Samuel Fanči and Hugo Hrbáň — always great to see you!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🤝 It was a real joy to reconnect with my PhD supervisor and mentor @gjbarton.bsky.social, as well as former colleagues @stuartmac44.bsky.social, @foreveremain.bsky.social, @mitsenkov.bsky.social, Vanessza Fentor, Douglas Freeburn, @tanmayee.bsky.social and @rosiegallagher.bsky.social!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🙏 Sincere thanks to conference organisers, COSI chairs, reviewers and all the outstanding speakers in my session — including @nbordin.bsky.social, Hanne Zillmer and Miguel Fernandez — for inspiring talks on #structural #domains, the #pocketome and #biophysical limits of the #protein #universe!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🎤 A special year — I had the honour of speaking at #3DSIG before 100+ peers, sharing three main #PhD projects, each published. A perfect wrap-up to six incredible years in the @bartongrp.bsky.social at the University of Dundee before starting a new chapter!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🧳 Fourth year in a row after #Sitges 2022, #Lyon 2023, and #Montreal last year. As always, it was intense, exciting, and enriching — the top place to stay current, spark ideas, reconnect with peers, and celebrate discovery in computational biology!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025

🌍 A couple of weeks ago, I had the pleasure of attending the annual #ISMB + #ECCB, international Conference on Intelligent Systems for Molecular Biology, organised by @iscb.bsky.social which took place in the magical city of #Liverpool!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 25/07/2025

Merci, crack! Després de conc anys, ja hi hem arribat. Ara comença la propera aventura!

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