iiinova — where your digital self keeps evolving

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

🧵 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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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

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

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

🎉 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

🌍 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

🎓 📚 Last month, I was awarded my PhD degree by the University of Dundee. This marked the end of my 10-year journey as a student and closed an important chapter of my life in Dundee — a journey that began in 2017 as an #Erasmus exchange undergraduate student.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 11/07/2025

The @narjournal.bsky.social Annual Web Server Issue is now finalised. Congratulations to all other authors for their excellent resources. I am thrilled to share that one of our #LIGYSIS-web paper figures was selected as the cover image for this issue. Check it out here: lnkd.in/dXAb6jwv!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 01/07/2025

🎉 I am thrilled to share that our latest work on is now publicly available on @biorxivpreprint.bsky.social. The title is "Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish ints interaction with the Ser/Thr kinase CK1α". 🔗 Pre-print: www.biorxiv.org/content/10.1...

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

My #PhD #Thesis: "Computational methods for the characterisation and evaluation of protein-ligand binding sites" is now #publicly #accessible! I also shared the #GitHub #repository I used during the writing period. 📖 Thesis: tinyurl.com/utges-thesis 🔗 Repo: tinyurl.com/utges-thesis...

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 04/06/2025

I'll be attending the @iscb.bsky.social #ISMBECCB2025 conference in Liverpool from July 20-24. Who else is coming? Register here and don't miss it. It's going to be great! invt.io/1bxbm6fohph I'll present my PhD work at the @bartongrp.bsky.social on protein-ligand interactions at the 3DSIG panel!

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Reposted by Dr Javier Sánchez Utgés

Jalview @jalview.bsky.social · 03/06/2025

🌼 Jalview and The Daffodil DNA Project were at the 2025 Conference @associationscied.bsky.social this weekend with colleagues from James Hutton. 🧬Lots of chats with folks about all things bioinformatics, DNA sequencing, multiple sequence alignment and protein structure!

Jalview, Daffodil DNA and James Hutton Institute exhibition booths at the ASE 2025 Conference in Cupar, Scotland.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 19/05/2025

I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out! 📜 : tinyurl.com/utges-LIGYSI...

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/05/2025

Accessing a wealth of structure data to integrate with your #MSA is possible accessing the #3DBeacons network through #Jalview. Get experimentally determined structures from @pdbeurope.bsky.social as well as predicted structure models from #AlphaFoldDB, @swiss-model.bsky.social and other providers!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 16/05/2025

Two weeks ago, I reached a significant #milestone my career, marking my most substantial #achievement yet. Following four and a half years of dedicated work at the University of #Dundee and a successful #PhD viva defence, I attained the title of Doctor of Philosophy in #Structural #Bioinformatics

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 14/05/2025

With Jalview you can explore how genetic variants map to protein structure - directly from the multiple alignment of both coding DNA and protein sequences. Seamlessly integrate your structure viewer and dive into the molecular story of the sequence! From ACGT to 3D — Jalview takes you all the way!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 13/05/2025

What a day this was! Filled with emotions with colleagues, friends and family present and ending a really important chapter of my life. Happy with the work we did and thankful for what Dundee, the University, the School and this excellent Division has brought to my life in the last 6 years!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 23/04/2025

#Jalview goes the extra mile! Remember the integration with @chimerax.ucsf.edu or #PyMOL? Well, you can use these viewers to inspect #AlphaFold confidence scores #pLDDT and #PAE in multiple #sequence alignment and #structure! Multiple structure prediction confidence analysis made easy with Jalview!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 11/04/2025

I love the @chimerax.ucsf.edu #tile view. Such an elegant and dynamic way to visualise multiple structures at the same time. Here are 32 #biological #assemblies of bovine rhodopsin #P02699 (www.uniprot.org/uniprotkb/P0...) beautifully structurally aligned and downloaded from @pdbeurope.bsky.social.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/04/2025

It was so great to meet the #researchers behind some of the most #novel, #relevant and #impactful work in the protein-ligand interactions field. This picture was taken a few weeks ago at the @iscb.bsky.social #3DSIG + #ELIXIR #3DBioinfo meeting at @bsc-cns.bsky.social in #Barcelona! PLIs #Avengers!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 09/04/2025

I have already submitted mine. Still months away, but I am so excited! Join us in Liverpool for a great conference!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 26/03/2025

🧬 FAMILY PICTURE 📸 It was so nice that my #PhD #supervisor @gjbarton.bsky.social came to support me to the @iscb.bsky.social #3DSIG + #ELIXIR #3DBioinfo meeting last week in Barcelona. Mike Sternberg was there too and I managed to get the family picture I wanted. Mike was Geoff’s PhD supervisor! 🎊

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 24/03/2025

It was a pleasure and honour to give a talk at the #ELIXIR #3DBioinfo + @iscb.bsky.social #3DSIG meeting last week in @upc.edu and @bsc-cns.bsky.social in beautiful #Barcelona. I presented my PhD work in the @bartongrp.bsky.social in the #SLS of #Dundee on protein-ligand interactions.

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Reposted by Dr Javier Sánchez Utgés

Hajk-Georg Drost @hajkdrost.bsky.social · 23/03/2025

Deadline was just extended to 30th March! :)

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 23/03/2025

What a great event this was: #ELIXIR #3DBioinfo + @iscb.bsky.social #3DSIG bringing together the two communities of interest of structural bioinformatics. A great selection of speakers and posters and the best way to find out what’s going on in the field. And no better place than Barcelona to do so!

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Reposted by Dr Javier Sánchez Utgés

Janani Durairaj (Jay) @ninjani.bsky.social · 08/02/2025

We’ve been benchmarking deep learning co-folding methods for protein-ligand complex prediction, leading to the creation of 🌹Runs N’ Poses🌹. Great effort by @peterskrinjar.bsky.social and @jeeberhardt.bsky.social putting this together so quickly. Please have a look, excited for community feedback!

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Reposted by Dr Javier Sánchez Utgés

Jalview @jalview.bsky.social · 11/03/2025

👩‍🎓Last month, 60% of our YouTube audience was women. This International Women's Day, we are celebrating all the trailblazing women who watch our training videos online. 💕 Thank you for supporting our educational content! Watch here: www.youtube.com/@jalviewtrai... #IWD2025 #AccelerateAction

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 04/03/2025

As my PhD journey comes to an end, I can say I have no regrets. These 6 years in the @bartongrp.bsky.social in Dundee have been an immensely enriching experience. I believe @hajkdrost.bsky.social has a spark and vision and talent and an opportunity of working with him is truly worth considering!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 24/02/2025

PhD Thesis submission ✅ Today I submitted my PhD Thesis “Computational methods for the characterisation and evaluation of protein-ligand binding sites” achieving a significant milestone in my career and the culmination of the last 4.5 years of my life. Thanks to everyone that helped me on the way!

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Reposted by Dr Javier Sánchez Utgés

BSC-CNS @bsc-cns.bsky.social · 19/02/2025

ELIXIR 3DBioinfo Annual General Meeting | ISCB 3DSig 2025 🧬💻BSC hosts this meeting that brings together structural bioinformatics researchers from 2 communities, 3D-BioInfo & 3D-SIG, for networking & to exchange ideas ➡Check out the agenda: www.bsc.es/ZCz

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 19/02/2025

Same, really looking forward to it. Great speakers in the programme and always great to visit home in Barcelona. Also I’ll be giving a short talk about the work I’ve been doing during my PhD. Join us for a great three days of science in beautiful #Barcelona!

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Reposted by Dr Javier Sánchez Utgés

Colin Carroll @colcarroll.bsky.social · 13/02/2025

Everything's crazy, so I implemented fractals in @matplotlib.bsky.social. Getting the transform API right, and figuring out how to repeatedly apply a function in Python were the hard parts. colab here if you want to try it out: colab.research.google.com/drive/10mzOt...

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Reposted by Dr Javier Sánchez Utgés

Parc de Recerca Biomèdica de Barcelona @prbb.org · 12/02/2025

2⃣ estudios recientes del @crg.eu se centran en la estructura proteica. 🧬Uno, para entender las enfermedades, liderado por @benlehner.bsky.social y con la empresa BGI de Shenzen. 🌳El otro, para determinar mejor los árboles filogenéticos, liderado por Cedric Notredame. Más ℹ️👇

tuit.cat

La estructura proteica, clave en la evolución y la salud - El·lipse

Dos estudios del CRG se centran en la estructura proteica para entender las enfermedades y elucidar árboles filogenéticos, respectivamente.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 12/02/2025

No trade-off between speed and accuracy. P2Rank can do both. Brilliant work, @rdkbio.bsky.social and colleagues!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 07/02/2025

I didn't know that... Or did I? You can pretty much do anything in sequence and structure analysis with Jalview! ANYONE: "Hmmm, I wonder if I could cluster a group of sequences by features such as predicted ligand sites and then analyse amino acid conservation within each group..." 🤔 #JALVIEW: YES

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Marian Novotny @majek.bsky.social · 05/02/2025

Things are often obvious, but sometimes less so. It is true also for small things like ligand-binding sites. In this work, our @cusbg.bsky.social group presents a new dataset designed for cryptic-binding site predictons - happy, to be part of this: academic.oup.com/bioinformati...

academic.oup.com

CryptoBench: cryptic protein–ligand binding sites dataset and benchmark

AbstractMotivation. Structure-based methods for detecting protein–ligand binding sites play a crucial role in various domains, from fundamental research to

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Reposted by Dr Javier Sánchez Utgés

Marian Novotny @majek.bsky.social · 16/01/2025

Welcome a new doctor! My student has successfuly defended his thesis on diversity of ligand binding sites today! Congratulations, Christos Feidakis!

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Reposted by Dr Javier Sánchez Utgés

Diego del Alamo @delalamo.xyz · 13/12/2024

Protenix, the AF3 reproduction made by TikTok's parent company ByteDance, is now available for commercial use with an Apache 2.0 license

github.com

GitHub - bytedance/Protenix: A trainable PyTorch reproduction of AlphaFold 3.

A trainable PyTorch reproduction of AlphaFold 3. Contribute to bytedance/Protenix development by creating an account on GitHub.

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 05/12/2024

Well done, Gonzalo! Congrats on the Ramón y Cajal! You deserve it!

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Reposted by Dr Javier Sánchez Utgés

Kate Michie @kmichie.bsky.social · 17/11/2024

So many people added to pack 1 this weekend we had to make pack 2. Makes sure you refresh for followers on pack one to see them all! 🧶🧬 go.bsky.app/DDetSBp

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 29/11/2024

The new revamped enhanced #PDBe-KB Ligand Pages just looks great! So information rich to offer biological context for any ligand! 🔗 : www.ebi.ac.uk/pdbe-srv/pdb... 📜 : www.biorxiv.org/content/10.1... Congrats and thanks #Preeti and the rest of @pdbeurope.bsky.social for this and all resources!

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 26/11/2024

#RenderCV is such a cool and #easy way to generate a CV. It uses a #YAML input file to generate a CV with #LaTex. 🔗 github.com/JavierSanche... Check out how easy it is with this repo! Thanks @tanmayee.bsky.social for recommending the tool and @rdkbio.bsky.social for recommending I make a repo!

github.com

GitHub - JavierSanchez-Utges/JSU-CV: This is a GitHub Repository with my CV generated with RenderCV

This is a GitHub Repository with my CV generated with RenderCV - JavierSanchez-Utges/JSU-CV

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Dr Javier Sánchez Utgés @javierutges.bsky.social · 25/11/2024

Really cool way to spell things with the #Protein #Alphabet created by @davhox.bsky.social! You can find it here: davidhoksza.github.io/BioAlphabet/ Now, back to work, before I lose my whole day playing with this... Any chance to find out the PDB IDs or files for these letters? Thanks, David!

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Su-In Lee @suinlee.bsky.social · 23/11/2024

Here is a #compbio starter kit! go.bsky.app/QVPoZXp To all the #Bioinformatics #Genomics #MachineLearning folks: please RP and let’s build this together!

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