Bijvoet Centre

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

We are happy to be hosting John Christodoulou, of University College London, @ucl.ac.uk, today for a Bijvoet Seminar entitled "Structural investigations of protein folding on the ribosome".

In memoriam: Hans Vliegenthart In memoriam: prof. dr. Hans Vliegenthart (April 7, 1936 – February 12, 2026)

With sadness we share the passing of em. prof. dr. Hans Vliegenthart, founder of the Bijvoet Centre for Biomolecular Research at Utrecht University. His scientific legacy will continue to inspire.
In memoriam: www.uu.nl/en/news/in-m...

We are happy to be hosting David Dulin, @dulinlab.bsky.social, of @vuamsterdam.bsky.social today, for a Bijvoet Seminar entitled "Leveraging high-throughput magnetic tweezers to investigate coronavirus replication at the single-molecule level".

The Dutch Research Council (NWO) announced large investments in 11 (inter)national research infrastructures this week, and we are very happy that includes investments in our electron microscopy and mass spectrometry facilities, through projects EMPower and BioBeyond-NL:

www.nwo.nl/en/news/nati...

We are happy to be hosting Alex Volkov of the Vrije Universiteit Brussel today, for a Bijvoet Seminar entitled "When chemistry meets biology: a travel to the protein multiverse".

Today, the Dutch nodes of the European Life and Medical Science Research Infrastructures discuss their strategy and sustainability for the future at @naturalis.bsky.social in Leiden. We are representing @instruct-eric.bsky.social and structural biology.

Only a few days left to apply for our EMBO course with a great lineup of speakers and tutors! Please feel free to RT!

Course website: meetings.embo.org/event/25-bio...

Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social

Location: www.ibg.edu.tr

pytom-match-pick: A tophat-transform constraint for automated classification in template matching Template matching (TM) in cryo-electron tomography (cryo-ET) enables in situ detection and localization of known macromolecules. However, TM faces cha…

Automated detection of macromolecules in cryo-ET data of cellular samples is challenging. Here, we introduce "pytom-match-pick", a GPU-accelerated, open-source interface that improves the efficiency and accuracy of macromolecule detection in cellular contexts: www.sciencedirect.com/science/arti...

Launching Thermo Fisher Scientific's Krios 5 Cryo-TEM | A New Era in Electron Microscopy YouTube video by Sensu

The artists from Sensu have worked with @thermofishersci.bsky.social and made this beautiful video on the applications of structural biology: www.youtube.com/watch?v=m3QA...

Check out our YouTube channel for videos we made with Sensu about our work: www.youtube.com/@BijvoetCenter

Indeed I'm happy to be here! Looking forward to great science 💪🏼

We are happy to host, on behalf of the Netherlands, the Council meeting of Instruct-ERIC (@instruct-eric.bsky.social), the European Research Infrastructure Consortium for structural biology. If you are interested in accessing state of the art structural biology technology, see instruct-eric.org.

We are very happy to have Christoph Müller from the EMBL (@embl.org) as the final speaker of the joint session of Instruct-ERIC (@instruct-eric.bsky.social) and the Bijvoet Centre at the 2025 Bijvoet Symposium!

Delighted to be in Utrecht to learn from our users in the Netherlands, we can always do better!!

@utrechtuniversity.bsky.social @nkinl.bsky.social @necen.bsky.social

The next speaker this afternoon is Michael Leung of @hubrechtinstitute.bsky.social, who conducted Cryo-EM studies at NeCEN in @unileiden.bsky.social through Instruct!

instruct-eric.org/centre/necen...

Since this month, Eva Bertosin (@thedneva.bsky.social) has joined the Bijvoet Centre, bringing her expertise on biophysics and DNA origami. Welcome Eva!

Beautiful and inspiring talk by Sheena Radford of the @radford-lab.bsky.social at the Astbury Centre for Structural Molecular Biology (@astbury-bsl.bsky.social) from the University of Leeds (@universityofleeds.bsky.social) at our annual Bijvoet Symposium!

Great to have almost the entire Bijvoet Centre together for our 2025 Bijvoet Symposium! Looking forward to a lot of exciting science!

The manuscript describing the new modular version of HADDOCK is finally available as a preprint! The result of a team work over several years, supported by @bioexcelcoe.bsky.social @bijvoet-centre.bsky.social @esciencecenter.bsky.social - www.biorxiv.org/content/10.1...

Simultaneous polyclonal antibody sequencing and epitope mapping by cryoEM and mass spec: how far can we go? Check out the final version of our paper in eLife:
elifesciences.org/articles/101...

We are very happy to host Max Bonomi (@bonomimax.bsky.social) from the Institute Pasteur (@pasteur.fr) for a Bijvoet Seminar about structural and dynamic biology with integrative approaches.

#GBMLunch on April 23!
Speaker: Tzviya Zeev Ben Mordeha
@tzviyazbm.bsky.social from @bijvoet-centre.bsky.social

Title: Cryo-EM single particle analysis meets cryo-ET at the sperm tail
Chair: Cristina Paulino from
@uniheidelberg.bsky.social

Organized by the GBM Study Group "Structural Biology"

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer - Nature Communications While DIA has advanced standard proteomics, its application in glycoproteomics has remained limited. Here, the authors present an optimized narrow-window DIA method for N-glycopeptides, nGlycoDIA, ena...

In this recent publication, we used an Orbitrap Astral mass spectrometer to rapidly analyze plasma glycoproteins, identifying over 3000 glycoPSMs in 40 minutes, with potential for high-throughput clinical applications: www.nature.com/articles/s41...

The first project I worked on, right after joining @bijvoet-centre.bsky.social!

Interested in advanced therapeutics such as mRNA? See the latest work of Evolène Deslignière, doi.org/10.1016/j.om..., in collaboration with Pfizer, using innovative mass spectrometry & photometry @bijvoet-centre.bsky.social to obtain precision measurements on mRNA purity & structural integrity

Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus Reactive oxygen species (ROS) pose a significant threat to biological molecules, prompting organisms to develop systems that buffer oxidative stress and contain iron, which otherwise amplifies ROS pro...

And now to something completely different: the response of an anaerobic archaeon to oxidative stress. Tubular nanocompartments encapsulate virus-like particles! Great work by Wenfei Song and many colleagues from @bijvoet-centre.bsky.social and @mib-wur.bsky.social.
www.biorxiv.org/content/10.1...

Exciting Bijvoet Seminar by Marie-Eve Aubin-Tam from @tudelft.bsky.social on the engineering of bioinspired and living materials!

Consortium led by Markus Weingarth awarded €1.5 Million to tackle antibiotic toxicity Fundamentally understanding why some antibiotics turn out to be toxic is now a major step closer, thanks to a €1.5 million grant awarded to biochemist Markus Weingarth.

We congratulate Markus Weingarth of our #NMR spectroscopy group here at @utrechtuniversity.bsky.social with the recent award of a new #NWO funded project to tackle antibiotic toxicity.

www.uu.nl/en/news/cons...

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer Nature Communications - While DIA has advanced standard proteomics, its application in glycoproteomics has remained limited. Here, the authors present an optimized narrow-window DIA method for...

Just out by Shelley Jager: rdcu.be/edEnO. One of the fastest & deepest plasma glycoproteomics studies. Take home message; we even detect glycosylated cytokines and chemokines, but also still need better software. #glycotime @utrechtuniversity.bsky.social @bijvoet-centre.bsky.social

Liposome-Encapsulated Escherichia coli Lysates to Reconstitute Intracellular Macromolecular Crowding Effects Intracellular macromolecular crowding impacts biomacromolecule behavior, including oligomerization, phase separation, and diffusion. However, understanding crowding effects in cells is challenging as ...

In this recent study, we used liposomes with E. coli lysates to mimic cellular crowding. We were able to achieve physiological macromolecular crowding levels, creating a platform that enables the controlled study of physiological crowding effects.

pubs.acs.org/doi/10.1021/...