Dr Javier Sánchez Utgés
@javierutges.bsky.social
Postdoctoral Research Assistant in the @gjbarton.bsky.social Group at University of Dundee
Ligand site prediction benchmark: tinyurl.com/Utges-LBS
Fragment screening sites: tinyurl.com/Utges-FRAGSYS
Ankyrin repeats: tinyurl.com/Utges-ANKS
Ligand site prediction benchmark: tinyurl.com/Utges-LBS
Fragment screening sites: tinyurl.com/Utges-FRAGSYS
Ankyrin repeats: tinyurl.com/Utges-ANKS
Pinned
🎓 📚 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.
🌍 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!
August 6, 2025 at 12:24 PM
🌍 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.
July 25, 2025 at 3:15 PM
🎓 📚 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 one of our #LIGYSIS-web paper figures was selected as the cover image for this issue. Check it out here: lnkd.in/dXAb6jwv!
July 11, 2025 at 2:20 PM
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 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...
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...
July 1, 2025 at 1:51 PM
🎉 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...
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 also shared the #GitHub #repository I used during the writing period.
📖 Thesis: tinyurl.com/utges-thesis
🔗 Repo: tinyurl.com/utges-thesis...
June 6, 2025 at 9:19 AM
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 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!
I'll present my PhD work at the @bartongrp.bsky.social on protein-ligand interactions at the 3DSIG panel!
June 4, 2025 at 9:04 AM
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!
I'll present my PhD work at the @bartongrp.bsky.social on protein-ligand interactions at the 3DSIG panel!
Reposted by Dr Javier Sánchez Utgés
🌼 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!
🧬Lots of chats with folks about all things bioinformatics, DNA sequencing, multiple sequence alignment and protein structure!
June 3, 2025 at 2:36 PM
🌼 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!
🧬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...
📜 : tinyurl.com/utges-LIGYSI...
May 19, 2025 at 10:37 AM
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...
📜 : 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!
Get experimentally determined structures from @pdbeurope.bsky.social as well as predicted structure models from #AlphaFoldDB, @swiss-model.bsky.social and other providers!
🚀 Structure alert: Discover protein models in Jalview using the 3D Beacons network. Browse thousands of experimental and predicted structures from Protein Data Bank, AlphaFold, SWISS Model and more with the click of a few buttons!
▶️ Watch our instructional video: www.youtube.com/watch?v=ZBDZ...
▶️ Watch our instructional video: www.youtube.com/watch?v=ZBDZ...
Using 3D Beacons to access AlphaFoldDB, PDB and more in Jalview
YouTube video by Jalview & Dundee Resource Online Training
www.youtube.com
May 16, 2025 at 10:07 AM
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!
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
May 16, 2025 at 9:48 AM
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!
Seamlessly integrate your structure viewer and dive into the molecular story of the sequence!
From ACGT to 3D — Jalview takes you all the way!
👀 Visualise pathogenic variants in Jalview's protein-CDS split screen window as you map these onto your favourite 3D molecular viewer! We have PyMol, ChimeraX, UCSF Chimera and JMol available for your analyses.
Watch our 'Genome to Function' video to find out how: www.youtube.com/watch?v=e/6a...
Watch our 'Genome to Function' video to find out how: www.youtube.com/watch?v=e/6a...
May 14, 2025 at 5:56 PM
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!
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!
Congratulations to Javier @javierutges.bsky.social on his successful PhD viva today!
@bartongrp.bsky.social
@bartongrp.bsky.social
May 13, 2025 at 8:01 AM
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!
Multiple structure prediction confidence analysis made easy with Jalview!
💡Protein lovers - a brand NEW video exploring AlphaFold's pLDDT score in Jalview is out! Find out how you can select, hide and colour your alignments using this 3D structure prediction confidence metric.
▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...
▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...
April 23, 2025 at 3:23 PM
#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!
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.
April 11, 2025 at 12:53 PM
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!
April 9, 2025 at 11:49 AM
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!
We are getting so many great abstracts!! This year's programme will look fabulous! You can still be part of it!! There is still one more week to go to send your work to this year's 3DSIG!! Do not miss the chance!!!
Submit now!
t.co/gCPpDtpzD8
Submit now!
t.co/gCPpDtpzD8
April 9, 2025 at 10:37 AM
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 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! 🎊
March 26, 2025 at 5:59 PM
🧬 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 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.
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.
March 24, 2025 at 5:58 PM
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.
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.
Reposted by Dr Javier Sánchez Utgés
Deadline was just extended to 30th March! :)
Please spread the word🙏:
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
How do ancient genes regulate animal embryo development at single cell resolution | University of Dundee, UK
A PhD project at the University of Dundee
www.dundee.ac.uk
March 23, 2025 at 5:23 PM
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!
Everything comes to an end but memories remain!!
We had a great 3DSIG/3DBioinfo event in "sunny" Barcelona this week!! I have enjoyed so much to help organising it & to have such great minds all together sharing science for 3 days!!
Aufwiedersehen friends! For more science & friendships to come! ⭐
We had a great 3DSIG/3DBioinfo event in "sunny" Barcelona this week!! I have enjoyed so much to help organising it & to have such great minds all together sharing science for 3 days!!
Aufwiedersehen friends! For more science & friendships to come! ⭐
March 23, 2025 at 2:24 PM
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!
Reposted by Dr Javier Sánchez Utgés
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!
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 8, 2025 at 10:30 AM
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!
Reposted by Dr Javier Sánchez Utgés
👩🎓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
💕 Thank you for supporting our educational content!
Watch here: www.youtube.com/@jalviewtrai...
#IWD2025 #AccelerateAction
March 11, 2025 at 2:21 PM
👩🎓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
💕 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!
I believe @hajkdrost.bsky.social has a spark and vision and talent and an opportunity of working with him is truly worth considering!
Please spread the word🙏:
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
How do ancient genes regulate animal embryo development at single cell resolution | University of Dundee, UK
A PhD project at the University of Dundee
www.dundee.ac.uk
March 4, 2025 at 3:26 PM
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!
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!
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!
February 24, 2025 at 7:21 PM
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!
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!
Reposted by Dr Javier Sánchez Utgés
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
🧬💻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
February 19, 2025 at 10:15 AM
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
🧬💻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