Nature research paper: One-shot design of functional protein binders with BindCraft go.nature.com/46bhOAv

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...

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!

Watch out, one of the best in the field! 😀

We (meaning Aswin and Stan www.biorxiv.org/content/10.1...) found this jumbophage protein homologue of PhiKZ_124 that activates Avast5 and we solved a 2.1A cryoEM structure of but we have no idea what it does. Let me know it you got some idea. www.rcsb.org/structure/9RP3

My highest recommendation! Working with Martin is the ideal entry point into protein design.

Humanized Caffeine-Inducible Systems for Controlling Cellular Functions https://www.biorxiv.org/content/10.1101/2025.06.13.659463v1

Caffeine-regulated molecular switches for functional control of CAR T cells in vivo https://www.biorxiv.org/content/10.1101/2025.06.13.659487v1

Happy to share our first foray into the world of AI-based #ProteinDesign. www.biorxiv.org/content/10.1...

THIS IS HUGE! TWO Phase I HIV vaccine clinical trials have demonstrated that a stepwise mRNA-based vaccination strategy can SUCCESSFULLY activate AND advance immune responses toward producing broadly neutralizing antibodies (bnAbs), a CRITICAL milestone in HIV prevention. Let’s talk about that! 🧪🧵⬇️

"Adapting ProteinMPNN for antibody design without retraining" Our several-years-old fix to ProteinMPNN's tendency to make weird antibody CDR sequences is finally preprinted

Hi everyone! I’m a #NewPI just starting my lab and would love to hear your advice on lab management and building the lab culture. Any tips, lessons learned, or resources you’ve found helpful are very welcome! Feel free to reply, message me, or email me at rcastellsg(at)cnio.es thanks a lot!! 🤗

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”? If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein. Think I’ve finally found a way.

Programmable protein stabilization with language model-derived peptide guides www.nature.com/articles/s41...

You’ve heard of vibe coding—meet vibe protein design. Click, launch, and watch the binders roll in. That’s what we're unveiling with @ariaxbio.bsky.social today.

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...

Baker lab PyMOL config 👇

Thank you, Lennart! I'm very excited to join the newly founded Carl Zeiss Center for Synthetic Genomics and KIT with your lab nextdoor! Exciting times ahead!

I’m looking for a BTA and a Postdoc to help set up the Structural Biochemistry group at the Leibniz Institute for Immunotherapy (LIT) in Regensburg 😀. We apply synthetic biology and protein design to address key challenges in immunotherapy. lit.eu/work-with-us/ #SynBio #ProteinDesign #Immunotherapy

Job - Alert 🌱 ‼️ POSTDOCTORAL SCIENTIST (M/F/D) Deadline: 2025-04-06 Location: Germany, Regensburg, Bayern www.academiceurope.com/job/?id=7176 #hiring #Immunotherapy #Postdoc #LIT #syntheticbiology #proteindesign

new blogpost on protein binder design blog.booleanbiotech.com/protein-bind...

Hello bluesky

Hats off to all our american colleagues out there protesting in the streets today, scientific progress is the only way to a better future and no government should stand in the way of that ✊🏼

@synbio4allafrica.bsky.social #PlantSynBio education project will enable local students to sequence a native plant species and gain hands-on research and data analysis skills. They’ve secured ~76% of their microgrant. Now they need our help to cross the finish line: experiment.com/projects/exp...

I’m happy to share that I will join the LIT in Regensburg (lit.eu) as a Group Leader in Structural Biochemistry in May. We will combine synthetic biology and protein design to develop synthetic receptors and protein therapeutics to improve immunotherapy. Job openings will be available soon!

All-atom fixed backbone protein sequence design with FAMPNN @richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...

De novo design of transmembrane fluorescence-activating proteins pubmed.ncbi.nlm.nih.gov/39972138/ #cryoem

Abundant clock proteins point to missing regulation in the plant circadian clock www.embopress.org/doi/full/10.... first experimental determination of the abundance of transcription factors in Plants and for the circadian clock. It was such a challenge but finally out after peer review !!!

📢 New preprint, lead by Alex Bronstein, @sankethvedula.bsky.social and colleagues: Guiding AlphaFold with experimental data. This approach generates conformational ensembles guided by NMR, X-ray (or whatever) data. I am thrilled to tackle lots of exciting problems with it! arxiv.org/abs/2502.09372

Just now in Science: Researchers at the Institute for Protein Design report a computationally-designed, multi-step enzyme. Learn how they did it: www.asimov.press/p/ai-enzymes

🚨Preprint Alert!🚨 #ProteinDesign is advancing rapidly—wouldn't it be great to seamlessly combine design tools to achieve more than what each can do alone?🤔 Here, we introduce AI.zymes: A modular platform for evolutionary #EnzymeDesign.♻️🖥️ biorxiv.org/content/10.1... 1/🧵

Always a thrill to see your antibodies and structures in the wild 🤩@mfpronker.bsky.social www.sciencedirect.com/science/arti... pubs.acs.org/doi/full/10....

Making intrabodies from antibodies just got easier! Learn how we made 𝟭𝟵 intrabodies to bind and light up peptides and histone modifications in live cells. And thanks to Academia, all sequences are freely available. (video credit: Yuko Sato @YukoSatoT2) (1/15) www.biorxiv.org/content/10.1...

It is indeed striking how much AF3-based methods struggle to generalize to novel protein-ligand interfaces. It is also interesting that there remains a meaningful delta between AF3 and other reproductions at the most difficult generalization task (~25% vs ~13% success rate, so roughly double).

🚨New paper alert! 🚨 Our latest work in @cp-immunity.bsky.social shows that Ark313, an evolved AAV variant enables in vivo genetic engineering of murine T cells! 🧵👇 sciencedirect.com/science/arti...

🔬 Revolutionizing GPCR Design EPFL researchers develop a groundbreaking tool that factors in water-mediated interactions to engineer synthetic GPCRs, pushing protein design beyond natural limits. 🌍✨ read more: www.synbiobeta.com/read/computa... #Biotech #ProteinDesign #ScientificBreakthrough

Amazing work from Farren Isaacs team at Yale - reducing E.coli's genetic code down to only using a single stop codon. A 62 codon GRO with lots of potential for applications. www.nature.com/articles/s41...

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

Structural determinants of co-translational protein complex assembly www.sciencedirect.com/science/arti...

A “groundbreaking” therapy offering a potential cure for people living with Sickle Cell disease has been approved for use on the NHS. Clinical trials find 1-time gene therapy exa-cel offers ‘functional cure’ in 96.6% of patients. 🧪 #medsky www.theguardian.com/society/2025...

Immune cell sequencing from birth to old age "Using our lifecycle-wide single-cell dataset covering 13 age groups over the extent of the human lifespan...." www.nature.com/articles/s41...

Great to have @martinpacesa.bsky.social as invited speaker to our weekly Structural Biology Colloquia. Such a solid, functional and impactful workflow 🤩. Thanks a lot for coming!

Creating coveted bioluminescence colors for simultaneous multi-color bioimaging In Science Advances www.science.org/doi/10.1126/...

An opinion piece by @wouterhm.bsky.social , featuring ideas from all authors which are beautifully illustrated by @rborza.bsky.social : Unlocking the signaling potential of GPI-anchored proteins through lipolytic cleavage www.cell.com/trends/cell-...

Really interesting paper 🧪 🤩 Immune evasion through mitochondrial transfer 😮 Ikeda et al find that #mitochondria from cancer cells can #transfer over to T cells - altering their #metabolism & reducing antitumour immunity www.nature.com/articles/s41... www.nature.com/articles/d41... @nature.com

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview). 💾 github.com/steineggerla... 📄 www.biorxiv.org/content/10.1... 🐍 available in bioconda

We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!

Targeting protein–ligand neosurfaces with a generalizable deep learning tool | @Nature - MaSIF-neosurf can design binders for protein-ligand complexes, targeting neosurfaces (i.e., ligand-induced structural changes on the protein surface) Link: www.nature.com/articles/s41...