DSSNA: An Open-Source GROMACS Module for Automated Analysis of Nucleic Acid Secondary and Tertiary Structure in Molecular Dynamics Simulations https://www.biorxiv.org/content/10.64898/2026.09.25.754511v1

Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...

We are hiring! Start at a #MaxPlanckInstitute with your own independent Max Planck Research Group. This position is equivalent to a W2 Professorship at a German university, or Associate Professor internationally. 🔗Apply until October 14th! www.mpg.de/career/max-p... #ScienceCareer #MPRG #TenureTrack

In 2017 I co-organized a BPS thematic meeting on Conformational Ensembles from Experimental Data and Computer Simulations We're back in Berlin Aug 2027 with Biomolecular Dynamics: Integrating Experiments and Computation with a great line-up (to be revealed soon) www.biophysics.org/upcoming-the...

Thrilled to share that our paper describing protein-dependent frameshifting is now out in Molecular Cell @cellpress.bsky.social. Huge congratulations to @jemmabetts.bsky.social for publishing the first research paper from her PhD 🧬🧪🥳 www.sciencedirect.com/science/arti... 1/8

A protein-dependent riboswitch activates ribosomal frameshifting in cardioviruses

Programmed −1 ribosomal frameshifting (PRF) is a translational control mechanism used by RNA viruses to regulate the relative abundance of proteins en…

sciencedirect.com

Most PDB structures report one set of coordinates. But the experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble of structures. How to extract this ensemble data at scale has been a quest in structural biology for 40+ years.

Looks unorganized to you? It isn’t. Indeed, you are looking at fixed 3D structures of the cancer protein p53. It can adopt at least 50 different 3D structures and is much more ordered than previously thought! 🎥© @dszollosi.bsky.social l / MPI-NAT @compbiophys.bsky.social (1/3)

We are hiring an #IT expert! Interested to join our department @mpi-nat.bsky.social in #Göttingen 🇩🇪 as Hardware Operations Technician (IT-Systemtechniker*in)? Please apply! 📩 #joboffer #job #openposition 🔗 www.mpinat.mpg.de/5292977/23-26 📅 Don't miss the application deadline: August 23, 2026

If anyone is looking for a postdoc/staff scientist with experience in evolutionary genetics, computational biology/bioinformatics, and/or various omics methods (RNA-seq, Ribo-seq, LC-MS/MS), I'm still looking! (1) doi.org/10.1126/scie... (2) doi.org/10.1073/pnas... (3) doi.org/10.1371/jour...

🎉 We are delighted to see our latest #publication online introducing a #MM model that reconciles the decade-long bi-site versus tri-site controversy, showing that both pathways contribute depending on #ATP concentration. #F1-ATPase @springernature.com 🔗 www.nature.com/articles/s41...

A minimal chemo-mechanical Markov model for rotary catalysis of F1-ATPase - Nature Communications

F1-ATPase is a rotary motor protein essential for cellular energy transduction. Here the authors develop a thermodynamically consistent Markov model that quantitatively matches experimental data and r...

nature.com

THERE IS AN ACTIVE POGROM IN NORTHERN IRELAND. FASCISTS IN SKULL MASKS ARE GOING DOOR TO DOOR PULLING MIGRANTS OUT OF THEIR HOMES AND SETTING THEM ON FIRE.

New paper in @natcomms.nature.com! We show how the Clostridia peptide CliM acts as a molecular handbrake to monitor YidC activity. Cryo-EM & MD show it stalls the ribosome using diverse mechanisms until membrane insertion releases it. Paper: www.nature.com/articles/s41...

Diverse mechanisms of translation arrest by a Clostridia ribosome stalling peptide CliM - Nature Communications

CliM is a ribosome arrest peptide in Clostridia. Here, the authors show that CliM adopts helices and extensively interacts with the ribosome. The penultimate residue sterically blocks A-site accommoda...

nature.com

Are you interested in understanding protein dynamics and allostery in biomedically relevant "loopy" enzymes? We are looking for postdocs to join our group at GT for both applied and method development work. If you are interested, please email me your CV, cover letter, and details of 2-3 referees.

🎗️ Final reminder! This Sunday 31st May is the deadline: 💰 Early-bird registration 🗣️ Oral presentation abstract submission ➡️ bioexcel.eu/hzr0 #ComputerSimulation #conference #community

Mitochondrial ribosomes follow a precisely timed 🕺choreography to coordinate protein production, folding & insertion. 👉 About the collab between Peter Rehling (University Medical Center Göttingen) & our project group leader @niels-fischer.bsky.social & their teams: www.mpinat.mpg.de/5263150/pr_2...

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

From possibility to precision in macromolecular ensemble prediction - Nature Methods

This Perspective discusses current challenges in macromolecular ensemble prediction and the infrastructure and methodological advances needed to overcome these barriers.

nature.com

Over the past 5 years, 50 structures of full-length HECT-type ligase constructs have been deposited in the PDB. What have we learned from these studies, and what key questions remain open? Check out our new review on this exciting and fast-moving field: www.jbc.org/article/S002...

HECT-type ubiquitin ligases: Emerging principles in the era of full-length structures

Ubiquitin coordinates a complex network of cellular pathways through covalent modification of substrates. Specificity in substrate recognition and modification choice is largely conferred by ubiquitin...

jbc.org

I am organising a 2 day workshop on explainable AI as applied to (bio)chemistry in Copenhagen, June 15-16, 2026. Everyone is invited. No need to register, but lunch is at your own expense. #compchem

We are happy to share our latest publication with you that just appeared in J. #Proteome Res. @pubs.acs.org pubs.acs.org/doi/10.1021/... 🙏 Many thanks for the great collaboration with our colleagues @mpibiochem.bsky.social in Martinsried! #proteomics #IMS #MD #peptides

Bimodal Peptide Collision Cross Section Distribution Reflects Two Stable Conformations in the Gas Phase

Recent high-throughput applications to shotgun proteomics have shown great benefits of coupling ion mobility spectrometry (IMS) to mass spectrometry. IMS adds a separation dimension by differentiating...

pubs.acs.org

We open up to two Junior PI positions at UCT Prague, Czechia @vschtpraha.bsky.social. Broadly defined chemistry-related projects will be considered. A support from any department must be negotiated prior application. Feel free to contact me for further info or visit www.vscht.cz/research/dag....

We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...

Our latest contribution is out! In this highly collaborative paper, we show that tRNAs with a 4-base-pair anticodon stem are surprisingly frequent across organisms. Our atomistic MD simulations reveal the role of the 5th base pair. academic.oup.com/nar/article/...

Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis

Abstract. Recently, a tRNATrpCCA with a 4-base-pair (bp) anticodon stem (AS) was shown to efficiently recognize a near-cognate UGA codon in unicellular euk

academic.oup.com

#KeinVergessen: Heute vor zwei Jahren, am 25. März 2024, verübt ein Rechtsextremer einen rassistischen Brandanschlag in Solingen, bei dem İsmail (Kancho) Zhilov & Kıymet (Katya) Zhilova sowie ihre Töchter Elis (Emily) & Gizem (Galia) ums Leben kommen. https://f.mtr.cool/zfvsjdkdak

Our new FEP sampling engine GrandFEP is now on GitHub and Chemrxvi. We implemented GCMC, Water-Swap MC, REST2, and terminal-flip MC in OpenMM. Github github.com/deGrootLab/G... Chemrxiv doi.org/10.26434/che...

🚨 Preprint alert! We solved the structure of human NSUN2 bound to Asp tRNA, revealing how it installs m⁵C and recognizes RNAs #CryoEM #RNABiology A collab between Casañal & Gullerova labs, with @miclass.bsky.social and me working side by side as co-first authors 🔗 doi.org/10.64898/202... (0/7🧵)

Our recent investigation of the constriction in the bacterial ribosomal tunnel is online. Unbiased all-atom MD simulations of the entire ribosome and PDB analysis show, how flexible the constriction is. The flexibility is modulated by short nascent polypetides.

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 7mo ago

Early nascent polypeptide dynamics are coupled to the flexibility of the ribosomal tunnel constriction https://www.biorxiv.org/content/10.64898/2026.03.10.710814v1

We are looking for RNA enthusiasts to join us at the @uniregensburg.bsky.social as a junior group leader! Our university offer excellent infrastructure and collaboration opportunities for ground breaking RNA research. Please RT @jrrnascientists.bsky.social @rnasociety.bsky.social

We are recruiting a computational scientist for a postdoc position to work on detecting RNA modifications using nanopore sequencing: tinyurl.com/RiboComp Deadline March 4th. Please share and repost! More on the group: www.bric.ku.dk/research-gro...

Computational Postdoc in Ribosome Specialization at the Biotech Research and Innovation Centre

We are looking for a highly motivated and dynamic computational postdoc for a 3-year position to join the Lund Group. Our research Our team aims to understand h

tinyurl.com

The Faculty of Physics @uni-goettingen.de annually awards the Berliner-Ungewitter Prizes. Congratulations to Annke de Maeyer who receives this award for her exceptional master’s degree👏! We are happy she continues her PhD with us @compbiophys.bsky.social