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Janani Durairaj (Jay)

@ninjani.bsky.social
1.4K followers 414 following 49 posts

Deep learning for protein structure, interactions and design. University of Lausanne pickybinders.org

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Reposted by Janani Durairaj (Jay)
Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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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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European Conference on Computational Biology @eccb-europe.bsky.social · 04/09/2026
Congrats to ECCB proceedings paper winners: Daniil Litvinov (University of Basel & SIB) Zhi Wei (New Jersey Institute of Technology) Himmi Lindgren (University of Turku) Xian Yu (University of Hong Kong) Ying-Ju Lai (University of Pittsburgh) See all: academic.oup.com/bioinformati... #ECCB2026
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Reposted by Janani Durairaj (Jay)
Torsten Schwede @torstenschwede.bsky.social · 31/08/2026
Can we predict the stoichiometry of proteins in a complex from their sequences - fast and accurately? Congratulations to the #ECCB2026 🧬 proceedings paper award 🎉 @daniil-litvinov.bsky.social @ninjani.bsky.social @cellarchlab.com academic.oup.com/bioinformati...
Proceedings paper “Stoic: fast and accurate protein stoichiometry prediction”
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Janani Durairaj (Jay) @ninjani.bsky.social · 28/08/2026
Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!
compare, predict, design
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Etowah Adams @etowah0.bsky.social · 21/08/2026
OpenBind intends to collect 10,000s of protein-ligand structures & affinities. To prioritize what we collect next, we need cofolding models trained on the latest data. Today we're releasing OpenBind-0 and 717 new ligand-bound structures.
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Reciprocal Space Station @rs-station.bsky.social · 21/07/2026
1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!
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Pedro Beltrao @pedrobeltrao.bsky.social · 14/07/2026
Team science preprint, exploring the capabilities and limitations of Alphafold3 across different application areas, including protein-RNA, protein-lipid, ubiquitination,TCR and antibody recognition with @ninjani.bsky.social @labvanni.bsky.social @dgfeller.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas
Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling v...
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Reposted by Janani Durairaj (Jay)
Martin Pacesa @martinpacesa.bsky.social · 15/06/2026
Our lab website is finally online! pacesalab.com You can find information about our research, publications, and on-going developments in the lab.
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Pedro Beltrao @pedrobeltrao.bsky.social · 08/06/2026
Why AI-assisted research might have a lower impact that some estimate? I tried to look back at the rise of the internet and its impact on scientific research as a comparison point. I should stop spending time on this but condensing this info also helps me think www.evocellnet.com/2026/06/look...
evocellnet.com
Looking back at the rise of the internet to gauge the impact of AI-assisted scientific research
There is a lot of debate and some hyperbole around the impact of AI-assisted scientific research. When considering the future impact of gene...
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Janani Durairaj (Jay) @ninjani.bsky.social · 08/06/2026
Search with TEA 🍵 Against Many! → On the web: pickybinders.org/tea/steam → Locally: github.com/PickyBinders... Feedback welcome!
pickybinders.org
STEAM - Search with TEA against Many
Generated by create next app
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 06/06/2026
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe. 📄 www.nature.com/articles/s41... 💾 folddisco.foldseek.com​​​​​​​​​​​​​​​​ 🌐 search.foldseek.com/folddisco
nature.com
Structural motif search across the protein universe with Folddisco - Nature Biotechnology
Folddisco enables protein structural motif search in million scale databases.
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Janani Durairaj (Jay) @ninjani.bsky.social · 11/05/2026
It's finally out!
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Reposted by Janani Durairaj (Jay)
Mohammed AlQuraishi @moalquraishi.bsky.social · 08/05/2026
Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇
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Janani Durairaj (Jay) @ninjani.bsky.social · 13/04/2026
@lorenzopantolini.bsky.social and I are headed to @iclr-conf.bsky.social at Rio soon, with talks about this work at @gembioworkshop.bsky.social and LMRL workshops. Reach out to chat about representation learning for de novo protein design! 🫖
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Alisia Fadini @alisiafadini.bsky.social · 01/04/2026
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
rdcu.be
AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network
Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...
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Luca Jovine @jovinelab.org · 01/04/2026
Very happy to have had a chance to attack an initially very low-resolution #cryo-EM map with #ROCKET! Thank you again @alisiafadini.bsky.social and all other co-authors of this important work, which truly shows the power of combining experimental structural biology and #AI inference. rdcu.be/fa9YH
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Luca Jovine @jovinelab.org · 01/04/2026
Starting from an #AlphaFold-Multimer prediction, we used #ROCKET to build a model of ZPD, a homopolymeric zona pellucida (#ZP) protein, into an initial #cryo-EM map at only ~9 Å resolution. A subsequently obtained 4.6 Å map highlighted how superior the ROCKET model was over the initial prediction:
ROCKET enables model building of a ZPD filament from low-resolution cryo-EM
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Ben Engel @cellarchlab.com · 19/03/2026
Stoic 🦾 from our shared student @daniil-litvinov.bsky.social predicts protein complex stoichiometry. A fun collab with @ninjani.bsky.social @torstenschwede.bsky.social - this #AI adventure beyond our core #CryoET methods was made possible by the @biozentrum.unibas.ch PhD Fellowship Program! 🧪 🧶🧬
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Janani Durairaj (Jay) @ninjani.bsky.social · 19/03/2026
Check out this awesome work from @daniil-litvinov.bsky.social: Protein complex stoichiometry prediction (both homomers and heteromers) from sequence, with some nice ablations showing what makes the difference!
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Mohammed AlQuraishi @moalquraishi.bsky.social · 13/03/2026
New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
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Torsten Schwede @torstenschwede.bsky.social · 13/03/2026
Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.
The Critical Assessment of Structure Prediction (CASP) experiment is calling for prediction targets: Immune Complexes, Organic Ligand-Protein Complexes, Nucleic Acids and Complexes, Conformational Ensembles, Difficult Protein Structures and Complexes. 
Rule of Thumb: If AlphaFold3 can generate a high-quality model, it is likely not a CASP-grade challenge. If it struggles, we want it.
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Christian Dallago @machine.learning.bio · 26/02/2026
Five years ago, we released FLIP. The core question was: can ML models for protein fitness prediction generalize in the ways that actually matter for protein engineering, i.e. low data, extrapolation to more mutations, out-of-distribution sequences?
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Lorenzo Pantolini @lorenzopantolini.bsky.social · 11/02/2026
Remote homology and protein design: two sides of the same coin. Instead of finding remote homologs, we used TEA to design completely de novo proteins, folding into desired TEA sequences. I always love working with Jay, and “speed-running” this proof of concept was no exception.
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Janani Durairaj (Jay) @ninjani.bsky.social · 11/02/2026
A fun little idea that worked surprisingly well, using a structure-informed yet structure-independent alphabet for de novo protein design: www.biorxiv.org/content/10.6... 🧵(1/n)
biorxiv.org
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Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Stephanie Wankowicz @stephanieaw.bsky.social · 20/12/2025
open.spotify.com/episode/5EXO...
open.spotify.com
Science Tree Farm
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James Fraser @fraserlab.com · 29/12/2025
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...
fraserlab.com
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
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CAMEO-3D @cameo3d.org · 23/12/2025
🚀 New paper in @natmethods.nature.com! We present OpenStructure's powerful scoring capabilities, used to assess predictionsin CAMEO and CASP. Read the full study here: 🔗 doi.org/10.1038/s415... #StructuralBiology #Bioinformatics #OpenStructure #CASP #CAMEO #ProteinStructure
doi.org
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Janani Durairaj (Jay) @ninjani.bsky.social · 01/12/2025
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
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Mohammed AlQuraishi @moalquraishi.bsky.social · 28/10/2025
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
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Irina Bezsonova @irinabezsonova.bsky.social · 03/10/2025
This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social Day 2/31 Prompt WEAVE N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms. Pdb: 3UA0 Next prompt is CROWN and I would love your suggestions!
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Roni Odai @rodai.bsky.social · 02/10/2025
Viral AlphaFold Database (VAD) is live in Science Advances ~27,000 predicted viral protein monomers & homodimers Conserved folds across bacteria, archaea & eukaryotic viruses New toxin–antitoxin system KreTA uncovered Vast “functional darkness” remains uncharted www.science.org/doi/10.1126/...
science.org
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
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SIB Swiss Institute of Bioinformatics @sib.swiss · 10/09/2025
Océane Follonier​ @oceanef.bsky.social for “From bytes to binders: design, score and optimize​” #bc2basel #posterprize
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Torsten Schwede @torstenschwede.bsky.social · 27/08/2025
Critical benchmarking of structure prediction methods has been crucial for measuring progress and detecting breakthroughs. But how will the future look like? Join the discussion at our workshop in Basel on September 8 - just before the [BC]2 conference. @sib.swiss @biozentrum.unibas.ch ⬇️⬇️⬇️
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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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Janani Durairaj (Jay) @ninjani.bsky.social · 27/08/2025
Still some spots left, join us in Basel on Sep 8 (before [BC]2) to discuss structure prediction benchmarking and more!
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CAMEO-3D @cameo3d.org · 27/08/2025
🔬 Workshop: Future of Structure Prediction Benchmarking 📅 Sept 8, 2025 | Basel 💡 Talks + breakout sessions on #CASP #CAPRI #CAMEO & benchmarking for drug discovery 🎟️ Free registration (limited spots): lu.ma/ws9nu1xf Join us to explore how benchmarking can drive breakthroughs in structure prediction.
lu.ma
The future of structure prediction benchmarking: measuring progress and breakthroughs · Luma
Benchmarking has been a key driver of progress in protein structure prediction methods. As the field continues to evolve, several key questions prevail: How…
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EMBL Events @events.embl.org · 24/07/2025
Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl
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CATH-Gene3D @cathgene3d.bsky.social · 22/08/2025
CATH turns 30 years old this year! We are organising a 1-day symposium on September 16th at UCL, highlighting recent AI-based developments to enhance protein family classifications, annotations and analyses. www.eventbrite.co.uk/e/protein-an...
eventbrite.co.uk
Protein Annotations in the age of AI
A not-for-profit symposium hosted at UCL - more details about speakers and venue below.
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Kieran Didi @kdidi.bsky.social · 15/08/2025
AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6
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CAMEO-3D @cameo3d.org · 08/08/2025
Filtering out homologous structures from the PDB at 40% sequence identity is not enough to create a robust test set. Significant leakage persists at this level, and comparative modeling can still produce high quality models.
Scatter plot of LDDT as a function of sequence identity for high coverage homology models. The horizontal red line at 40% sequence identity highlights the presence high quality models in the low sequence identity region.
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Torsten Schwede @torstenschwede.bsky.social · 07/08/2025
Looking for a #fellowship for an independent #PhD at one of the best places for life sciences in the world? The summer call at @biozentrum.unibas.ch @unibas.ch is open until October 12, 2025. www.biozentrum.unibas.ch/phd/internat...
biozentrum.unibas.ch
Biozentrum PhD Fellowships
Share your passion for life sciences. If you are talented and highly motivated, want to broaden your horizons and are interested in a wide range of research topics, apply for one of the sought after B...
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Yo Akiyama @yoakiyama.bsky.social · 05/08/2025
Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
biorxiv.org
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
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Sergey Ovchinnikov @sokrypton.org · 05/08/2025
The big difference is in the pairing. The MMseqs2 server pairs sequences based on species, while our old HHblits MSAs were paired based on genome proximity (number of genes apart). Working w/ @milot.bsky.social and @martinsteinegger.bsky.social we implemented the proximity filtering in server (3/4)
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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
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Pat Walters @wpwalters.bsky.social · 22/07/2025
New Practical Cheminformatics Post patwalters.github.io/Three-Papers...
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Torsten Schwede @torstenschwede.bsky.social · 05/07/2025
We will be hosting a mirror site of the CASP data and workflows at @sib.swiss. Operating a redundant site with independent funding is a good idea for important scientific infrastructure, independent from the current funding situation in the US.
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Jason Nomburg @jnoms.bsky.social · 12/06/2025
Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
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