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Ajasja💻🧬🔬

@ajasjaljubetic.bsky.social
600 followers 335 following 59 posts

Research Assistant Professor, National Institute of Chemistry, Baker lab @ UW alumni, MSCA alumni. ljubetic-lab.si

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Computational and Structural Biotechnology Journal (CSBJ) @csbj.org · 09/06/2026
🔗BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists. Computational and Structural Biotechnology Journal (CSBJ). DOI: doi.org/10.34133/csb... 📚CSBJ - A Science Partner Journal: spj.science.org/journal/csbj @locbp.bsky.social @chem.uzh.ch #StructuralBiology #AI
🔗 BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0129

📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
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Jeffrey J. Gray @jeffreyjgray.bsky.social · 13/12/2025
In these pictures, we are at the historic castle of Bled…lab members Britnie, Natalia, Fatima and friend Rebecca are the antibody and I’m an antigen! Thanks to @ajasjaljubetic.bsky.social and Dominic Gront for being amazing conference chairs and hosts!
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Dr Ino Agrafioti @inoagrafioti.bsky.social · 09/12/2025
Once again, not enough money... so HUGE congratulations to LS1 @erc.europa.eu #ERCCoG grantees: @plaschkalab.bsky.social , Andreas Bock , Timm Fiebig , @wojtekgalej.bsky.social , Danny Nedialkova, Nataliya Petryk, @cryotud.bsky.social , @ajasjaljubetic.bsky.social ! You are TRULY extraordinary!
ky.social
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Jeremy Berg @jeremymberg.bsky.social · 10/11/2025
Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology. Transcript and video here www.cbsnews.com/news/researc...
cbsnews.com
Battle between Trump and universities hurting scientific research in need of federal funding
Federal research funding to universities has fueled breakthroughs for years. The White House is pressuring universities to align with the president's political agenda, or risk losing their funding.
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Acyn @acyn.bsky.social · 05/11/2025
AOC: We have a future to fight for, and we're either going to do that together or you're going to be left behind. It's not about Progressive. It's not moderate, it's not liberal. This is about do you understand the assignment of fighting fascism right now? And the assignment is you come together…
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Nature Portfolio @natureportfolio.nature.com · 26/10/2025
A Comment article in Nature Reviews Nephrology discusses how little attention has been given to how the termination of 2,100 NIH grants effect people who stand to benefit most from scientific discoveries: patients, care partners and community leaders. go.nature.com/47nCWmG #medsky 🧪
A quote on a blue background states, "The majority of the patients on our board interpreted this message to mean: 'Your life does not matter to us.'" The logo for "Nature Reviews Nephrology" is at the bottom.
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Amelie Stein @amelierocks.bsky.social · 20/10/2025
Fittingly, I arrived just in time for a talk from the organiser’s group @ajasjaljubetic.bsky.social 🚶‍♀️
Hotel banquet room with lots of round tables, lots of protein design aficionados, and an ongoing presentation on protein walkers
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ByteTrending @bytetrending.bsky.social · 06/10/2025
Protein Generation: AI Tools & Techniques Unlock next-gen protein design! Learn how cutting-edge AI is revolutionizing biomolecule creation, accelerating drug discovery & materials science. Explore innovative techniques for tailored protein generation – the future of innovation.
bytetrending.com
Protein Generation: AI Tools & Techniques
Unlock next-gen protein design! Learn how cutting-edge AI is revolutionizing biomolecule creation, accelerating drug discovery & materials science. Explore innovative techniques for tailored protein generation – the future of innovation.
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Kate Michie @kmichie.bsky.social · 02/10/2025
Just a heads up to anyone interested. @joshuamhardy.bsky.social will be presenting Protein DJ next week at the Australian Structural Biology Computing “Protein Design Seminars” hosted by @ausbiocommons.bsky.social www.biorxiv.org/content/10.1...
biocommons.org.au
WEBINAR SERIES: Leveraging deep learning to design custom protein-binding proteins — Australian BioCommons
Be inspired by case studies that show you how deep learning methods are speeding up the process of designing proteins with desirable biophysical properties. More information Register
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Biologic Models @biologicmodels.bsky.social · 23/09/2025
Do you have a colleague who just finished a major accomplishment and you'd like to commemorate their successes? 3D printed protein models with commemorative bases recognize your colleague's accomplishments in molecular biology. Submit a 3D print request at buff.ly/8x5f0BS
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UC Davis Egghead @ucdavis-egghead.bsky.social · 19/09/2025
AI has revolutionized study of protein structure and design. UC Davis researchers are taking part in two new NSF-backed projects to apply AI-driven protein engineering in industry. www.ucdavis.edu/news/federal...
ucdavis.edu
Federal Grants Support Research on AI-driven Protein Design
Two projects at the University of California, Davis, that use artificial intelligence to design and engineer proteins for industrial and health applications have been funded by the U.S. National Scien...
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Pure Science @purescience.news · 15/09/2025
AI reveals how toughest protein bonds behave #Science #Biology #MolecularBiology #ProteinResearch #Biotechnology #ArtificialIntelligence
purescience.news
AI reveals how toughest protein bonds behave
Proteins can form “catch-bonds” that tighten under force, much like a finger trap. Credit: Rafael C. Bernardi, Auburn Physics Researchers have used artificial intelligence to help uncover how certain...
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Martin Pacesa @martinpacesa.bsky.social · 04/09/2025
Really excited to receive the ERC Starting Grant! It’s gonna allow us to do a lot of cool protein design and structural biology method development in the next few years!
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Shashank Shekhar lab @sshekhr.bsky.social · 29/08/2025
📢📢Hiring 2 Research Assistants & 2 Postdocs at Emory University in Atlanta to study cytoskeletal biophysics/biochemistry. Please RT. RAs: great for recent bachelor's/master's in Physics/Bio/Chem/Biochem. Email CV and interests to shekhar@emory.edu. More info: www.shekharlab.org
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Martin Pacesa @martinpacesa.bsky.social · 27/08/2025
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...
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Dr. Lucky Tran @luckytran.com · 22/08/2025
The ideological cancellation of $800 million of scientific research grants because they supposedly focused on DEI was just backed by the Supreme Court. This is horrific on so many levels.
npr.org
Supreme Court allows NIH to stop making nearly $800M in research grants for now
But the court, in its emergency docket order, also left in place by a 5-4 order a lower court ruling that threw out NIH memos that enforced the administration's policies.
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Indrek Kalvet @ikalvet.bsky.social · 22/08/2025
RFdiffusion2 is now live! github.com/RosettaCommo... You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 19/08/2025
Early bird registration for 𝐄𝐔 𝐑𝐨𝐬𝐞𝐭𝐭𝐚 𝐂𝐨𝐧 𝟐𝟎𝟐𝟓 closes in two days! Come join us for three days of protein design fun! (October 20-22, 2025) Direct registration link: pretix.eu/SBD/RCon2025/ Website: europeanrosettacon.org
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Lars-Anders Carlson @lacarlson.bsky.social · 13/08/2025
Repost appreciated: Open #PhDposition in structural virology in my group! Join us in Umeå, Sweden to uncover how arboviruses remodel infected cells. In situ #cryoET and #cryoEM combined with #virology, #cellbiology, and #biophysics. Deadline 7 September. More info: www.carlsonlab.se/join/
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 11/08/2025
Due to popular demand (and summer time), early registration for EU Rosetta Con has been extended until Aug 20th! If you missed the deadline -- there is still time to apply: europeanrosettacon.org
europeanrosettacon.org
European RosettaCon
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New Scientist @newscientist.com · 10/08/2025
Researchers analysed thousands of natural protein sequences and got assistance from AI in order to design a new hydrogel adhesive that can stay sticky underwater or even within a living body.
newscientist.com
Super-sticky hydrogel is 10 times stronger than other glues underwater
Researchers analysed thousands of natural protein sequences and got assistance from AI in order to design a new hydrogel adhesive that can stay sticky underwater or even within a living body
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 01/08/2025
⏳ Time flies: only 10 days left for early registration to European RosettaCon 2025 (europeanrosettacon.org) from 20-22 Oct! The speaker lineup is shaping up amazingly well. Join us for three days of cutting-edge protein and biomolecular design topics!
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Florian Schueder @florianschueder.bsky.social · 31/07/2025
🚨 2 × PhD positions @EPFL! 🚨 Help us push the boundaries of fluorescence microscopy - DNA nanotech, custom optics & spatial omics in Lausanne 🇨🇭. Start Jan 2026. Send CV + motivation + 2 refs → fschueder@ethz.ch #PhD #Hiring #microscopy #SuperResolution #SpatialOmics #DNAPAINT #FLASHPAINT
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Instruct-ERIC @instruct-eric.bsky.social · 30/07/2025
Take a look at our speakers for the #IBBC2026! Registration is open and we are excited to see you all in Brussels next May! instruct-eric.org/ibsbc2026
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Kevin Drew @ksdrew.bsky.social · 29/07/2025
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell. www.biorxiv.org/content/10.1...
biorxiv.org
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
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Kate from Kharkiv @kateinkharkiv.bsky.social · 29/07/2025
Her name was Diana. She was 23 years old and 7 months pregnant. Russia murdered her today in an attack on the maternity hospital in Kamyanske.
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 23/07/2025
Happy to share the latest work from the lab, led by @mudgal17.bsky.social‬, in collaboration with the Weis lab @ethzurich.bsky.social. How do nuclear membranes fuse during NPC assembly? We answer this question in our latest work, where we identify a new mechanism for membrane fusion… (1/13)
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Patrick Bryant @patrickbryant1.bsky.social · 22/07/2025
Our study where we develop EvoBind2: Design of linear and cyclic peptide binders from protein sequence information is now published! www.nature.com/articles/s42...
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 21/07/2025
🎉🎉 ljubetic-lab.si🎉🎉 New lab website. We have been working on this in the background for a while, but now it's time to let it out :)
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Martin Pacesa @martinpacesa.bsky.social · 18/07/2025
Very interesting technique, will certainly try! Also great external validation of BindCraft, 7/36 binders bound, two with 0.8 and 6 nM affinity! Congratulations on the great work!
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Julien Capin @ju-cap.bsky.social · 17/07/2025
You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader? Check out our Cell-Free 2-Hybrid approach (CF2H) Full post: tinyurl.com/48cz5nb6 Preprint: www.biorxiv.org/cgi/content/...
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Seva Viliuga @proteinator.bsky.social · 17/07/2025
1/6 One of the key features of functional proteins is their inherent structural flexibility. In our recent work at #ICML, we introduce flexibility to protein structure design! More in a thread below. Code / Tutorial: github.com/graeter-grou... Poster: W-109, Thu 17 Jul 11 a.m. PDT — 1:30 p.m. PDT
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Rosetta Commons @rosettacommons.bsky.social · 16/07/2025
RFdiffusion: Beta Documentation Now Available We’re excited to announce that RFdiffusion now has official, Rosetta Commons-curated documentation! Read more: rosettacommons.org/2025/07/16/r...
rosettacommons.org
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 14/07/2025
We listened to your feedback. Proscuplt is: *Easier to install - now uses use containers 🚀 *Easier to run in SLURM - specify queue & task details directly in the prosculpt YAML file. github.com/ajasja/prosc... Big thanks to Federico Olivieri, Alina Konstantinova, Nej Bizjak, and Žan Žnidar🙏
github.com
Release v1.0.0 · ajasja/prosculpt
What's new Prosculpt now easier to install -- uses containers! Prosculpt now easier to run on SLURM -- all SLURM (queue, number of tasks) info can be given in the prosculpt yaml file. What's Chan...
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 14/07/2025
🎓 A proud lab moment: our very first master’s student defense is complete! Congratulations to David Krisper for achieving a flawless 10/10 — and thanks to his work mentor Eva Rajh for the wetlab guidance!🎉🎉🎉
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Ajasja💻🧬🔬 @ajasjaljubetic.bsky.social · 11/07/2025
One month left until early registration closes! Apply now if you would like to be considered for a talk. It will be an amazing conference bringing together leading scientists in the field of protein design. [Protein Emoji]
europeanrosettacon.org
European RosettaCon
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Microsoft Research @msftresearch.bsky.social · 10/07/2025
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 07/07/2025
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco
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Kai Johnsson @kjohnsson.bsky.social · 03/07/2025
Finally out in Nature Chem Bio: SNAP-tag2 for faster and brighter protein labeling www.nature.com/articles/s41... Thank you Steffi and Veselin.
nature.com
SNAP-tag2 for faster and brighter protein labeling - Nature Chemical Biology
SNAP-tag is a widespread tool for labeling protein for bioimaging. Now, Kühn et al. report SNAP-tag2 with increased labeling kinetics and brightness, which translates into a better performance in live...
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EMBO @embo.org · 07/07/2025
Learn about #AI tools in #protein #science, including design and engineering, at the EMBO Practical Course "AI for protein design" in Puerto Varas, Chile, 3–9 November 2025. Deadline: 1 August meetings.embo.org/event/25-ai-... #LifeSciences #research #training #ProteinStructure #EMBOevents 🧪
meetings.embo.org
AI for protein design
In the last 5 years, the scientific community has witnessed the development of several AI-based tools for groundbreaking advances in protein science. These tools have enabled scientists to predict pr…
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Dana 🌈🔬🪱 @millerlab.bsky.social · 03/07/2025
Fuck
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Don Vinh @donvinh.bsky.social · 03/07/2025
This will take the 🇺🇸 a few generations to rebuild from this.
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Science Magazine @science.org · 02/07/2025
Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90
scim.ag
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
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Martin Pacesa @martinpacesa.bsky.social · 30/06/2025
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...
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Rosetta Commons @rosettacommons.bsky.social · 30/06/2025
News from the Rosetta community: Prosculpt – an open-source library integrating RFDiffusion, ProteinMPNN, AlphaFold2 & Rosetta into one easy workflow More via @ajasjaljubetic.bsky.social : rosettacommons.org/2025/05/28/a...
rosettacommons.org
All about Prosculpt
by Ajasja Ljubetic Prosculpt is an open-source library that encapsulates RFDiffusion, ProteinMPNN, AlphaFold2, and Rosetta into an easy-to-use workflow. The input is a yaml file describing the prob…
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Rosetta Commons @rosettacommons.bsky.social · 30/06/2025
We are very excited to announce that early bird registration for European RosettaCon 2025 is now open! More information here: europeanrosettacon.org
europeanrosettacon.org
European RosettaCon
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 28/06/2025
Developing lenacapavir, the drug newly approved to protect against HIV for six months in one shot, took basic science, sophisticated chemistry, and perseverance www.science.org/cont...
science.org
Always ‘one atom away’: The long, rocky journey to an HIV prevention breakthrough
Developing lenacapavir, the drug newly approved to protect against HIV for six months in one shot, took basic science, sophisticated chemistry, and perseverance
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Diego del Alamo @delalamo.xyz · 27/06/2025
Tamarind has a web GUI for this app.tamarind.bio/tools/ablang...
app.tamarind.bio
Tamarind: Easy to use computational biology tools for scientists
State of the art computational tools for biology. Web server for bioinformatics tools. Tamarind allows biologists to access bioinformatics tools in protein design, molecular docking, and struct...
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