🌍 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!

🎓 📚 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.

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!

🎉 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...

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...

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!

🌼 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!

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...

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!

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

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!

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!

#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!

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.

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!

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

🧬 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! 🎊

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.

Deadline was just extended to 30th March! :)

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!

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!

👩‍🎓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

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!

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!

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

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!

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...

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👇

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

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

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...

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

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

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

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

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!

El CaixaResearch Institute empieza a fichar a científicos líderes en inmunología www.lavanguardia.com/ciencia/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!

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!

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!

Some fun with Boltz-1 (www.biorxiv.org/content/10.1...). I generated 1000 samples profilin (green) and compare them to the NMR structures (cyan). Samples were generated by docking 1000 random ligands. NMR structures show more conformational diversity.

A new version of CATH, v4.4, is out! 🎉 Here’s a link to the manuscript in NAR.

🚨 @enasequence.bsky.social! I would like to get the growth curve for the #European #Nucleotide #Archive. Basically replicate this curve. Is there anywhere I can access these data? Fellow Bioinformaticians, Computational Biologists and other nucleotide sequence geeks. Does anyone have this? Thanks!

To all my extended colleagues across the extended science social-verse, @enasequence.bsky.social is also available to be followed. Content and posts pending planning!

Our paper "Comparative evaluation of methods for the prediction of protein-ligand binding sites" is now published on Journal of Cheminformatics! 🔗 tinyurl.com/Utges-LBS On this paper we benchmark 13 original ligand site prediction tools and 15 variants on our curated reference dataset: #LIGYSIS!

Excellent, @jalview.bsky.social now on @bsky.app!

A starter pack for anyone interested in AI & drug discovery :) go.bsky.app/AgYHc8j

Our recent work TED: The Encyclopedia of Domains showcased by UCL: 365 million domain like structures identified in the AlphaFold DB, 194 million with proposed assignments to CATH superfamilies, plus a catalogue of domain-domain interactions. www.ucl.ac.uk/computer-sci...

Thought I'd start on @bsky.app with a thread about our paper on characterising #fragment #screening binding sites published on @natureportfolio.bsky.social Comms Bio This work sets the scene for our current work on #LIGYSIS Thread is from @gjbarton.bsky.social on X 🔗 tinyurl.com/Utges-FRAGSYS

Very nice #podcast by ISCB #Student #Council with Ana Castillo about the scientific journey of @gonzaparra.bsky.social, the impact #ISCB has had on it and some of the recent advancements in the field such as Google DeepMind's #Nobel #prize winner #AlphaFold. tinyurl.com/Parra-BioInf...