Joost Snijder

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PDB101: Molecule of the Month: Ebola Virus Proteins Structures of ebola virus proteins are giving new hope for fighting this deadly virus

The genome of ebola virus contains instructions for building seven proteins, which assemble with the genomic RNA to form one of the deadliest viruses.

Varicella-zoster virus reactivation and the risk of dementia - Nature Medicine Large-scale longitudinal health records reveal consistent association of varicella-zoster virus reactivation with dementia.

A new Nature Medicine study analyzing health records from >100 million people in the US offers compelling evidence that reactivation of varicella-zoster virus (VZV) ,the same virus that causes chickenpox and shingles may contribute to dementia risk.
www.nature.com/articles/s41...

PDB101: Browse: Immune System PDB-101: Training, Outreach, and Education portal of RCSB PDB

The bloodstream is filled with molecules and cells that search for invaders and destroy them if they are found. PDB structures have revealed how the immune system recognizes viruses and bacteria while leaving our normal molecules alone.
More at PDB-101:

Medicine Nobel goes to scientists who revealed secrets of immune system ‘regulation’ Mary Brunkow, Fred Ramsdell and Shimon Sakaguchi discovered cells that protect the body from autoimmune diseases.

This year’s Nobel Prize in Physiology or Medicine has been awarded to three scientists for discovering a class of immune cells that help to prevent the body from attacking its own tissues

go.nature.com/3VNrH1s

Cryo-EM resolves the structure of the archaeal dsDNA virus HFTV1 from head to tail This structure of an archaeal tailed virus (arTV) provides detailed insights into arTV assembly and infection mechanisms.

Out in Science Advances: Our #cryoEM structure of HFTV1, a virus infecting the halophile #archaea. *First full atomic structure (containing all structural proteins) of any tailed virus!* Congrats and thanks to all co-authors and our fantastic collaborators! www.science.org/doi/10.1126/...

Postdoctoral Research Assistant for the Biomolecular Design and Structural Nanomedicine Group DescriptionWe are looking for a Postdoctoral Researcher to join Roger Castells-Graells’ lab at the Spanish National Cancer Research Centre (CNIO). The successful candidate will work on innovative biom...

We’re looking for an enthusiastic postdoc to join our team. 😊

The project focuses on protein design and cryo-EM applied to cancer research. 🔬🧪

The position is fully funded for 3 years.

Please share 🙏

Job description and application details (deadline: October 11th): www.cnio.es/en/empleo/po...

Having a great time at msandm2025.org with a great bunch of people interesting in visualizing biomolecules, together with my co-chairs @joostsnijder.bsky.social @vixklen.bsky.social & Kyle Fort. Learning so much from all posters & lectures. We thanks all participants for joining us in Utrecht.

We’re hosting the MS+M conference in Utrecht today, lots of great talks ahead at the intersection of mass spec and microscopy. Here’s @hecklab.bsky.social kicking things off.

Congrats!

Structural Basis for Postfusion-Specific Binding to the Respiratory Syncytial Virus F Protein by the Canonical Antigenic Site I Antibody 131–2a The respiratory syncytial virus (RSV) fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and is responsible for mediating fusion between the viral…

SBGrid's eLife paper received a citation in August from @joostsnijder.bsky.social from @utrechtuniversity.bsky.social in @pubs.acs.org Infectious Diseases.

Read more here: buff.ly/0VRRJZz

#SBGrid #StayConnected #ScienceMatters

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Epstein–Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor - Nature Microbiology A genome-wide CRISPR screen helps to identify the Epstein–Barr virus receptor desmocollin 2 for primary epithelial cell infection. Additional infection assays revealed that desmocollin 3 also aids infection.

Epstein–Barr virus exploits desmocollin 2 as the principal epithelial cell entry receptor

www.nature.com/articles/s41...

Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!

#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.

Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

LRP8 is a receptor for tick-borne encephalitis virus - Nature LRP8, an apolipoprotein E and reelin receptor with high expression in the brain, is a receptor for tick-borne encephalitis virus.

www.nature.com/articles/s41...

Stunning work from the Chandran lab!

Zelfs als álle regeringsplannen slagen, krimpt het aandeel sociale huurwoningen De regering wil de komende jaren veel betaalbare huurwoningen laten bouwen. Maar zelfs als dat beleid goed wordt uitgevoerd, krimpt de sector.

De politiek zegt de volkshuisvesting in Nederland weer te willen versterken. Maar met de huidige plannen zal het aandeel sociale huurwoningen de komende jaren blijven krimpen.

Ik zette verschillende onderzoeksgegevens op een rijtje, Trouw schreef er een artikel over.

Een draadje:

Exciting day. We’re rebooting our advanced proteomics course. Full house, Kelly about to kick things off!

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...

Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)!
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM

RFdiffusion3 is here: www.biorxiv.org/content/10.1...

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail - Nature Communications Rodrigues and Queiroz et al. report the discovery of Naiavirus, the largest enveloped virus, isolated from a Brazil biome. With an oval capsid and flexible tail, its giant genome holds many novel gene...

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail
nature.com/articles/s41467-025-63463-6

One of our new manuscripts is now available on bioRxiv! Stay tuned!

Looks interesting (particularly for in silico affinity maturation) & code available on github: github.com/TencentAI4S/...

Our second paper explores the mechanism by which fusion-targeting antibodies neutralize the measles virus. It was exciting to integrate structural biology, virology, and biophysics to demonstrate that these F-targeting antibodies can provide complete protection against measles infection.

Veendam gooide de marktwerking overboord in de jeugdhulp en zie: de wachtlijsten verdwenen De doorbrekers, deel 3 | Jeugdhulp: In Veendam en omgeving waren door marktwerking wel 220 aanbieders van jeugdhulp. Overleg en samenwerking waren bijna onmogelijk – tot de gemeente besloot het helema...

Veendam gooide de marktwerking overboord in de jeugdhulp en zie: de wachtlijsten verdwenen www.nrc.nl/nieuws/2025/...

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

Zou er dan eindelijk een meerderheid zijn om wonen weer betaalbaar te maken? Maar eindelijk lijkt er een politieke meerderheid (zonder VVD) aan te komen voor maatregelen die wél werken.

Zou er straks dan eindelijk een politieke meerderheid zijn om wonen weer betaalbaar te maken? Om maatregelen te nemen die echt helpen? Ik nam de verkiezingsprogramma’s door en werd zowaar een beetje hoopvol.

Nieuwe column in @groene.nl, vandaag ook voor niet-abonnees

www.groene.nl/artikel/een-...

Remembering David Baltimore, a titan who transformed biology and spoke bluntly The influential Nobel laureate ran institutions, trained future scientific leaders, survived a scandal, and shaped policy

David Baltimore, for much of the past three decades, has been one of my most helpful, thoughtful sources. I wrote an obit about his remarkable career, and I included a few of my interactions with him. www.science.org/content/arti...

Great annual tradition to start off the academic year: The Vaccine Symposium at UMCU. Very interesting talk by Galit Alter on systems serology.