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Lars Bock

@larsvbock.bsky.social
1.5K followers 828 following 13 posts

Theoretical and computational physicist working on ribosomes and antibiotics - atomistic simulations, statistical physics and ML. Project leader at the MPI for Multidisciplinary Sciences t.co/1ecLGaOjXB 🚴

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Reposted by Lars Bock
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/09/2026
DSSNA: An Open-Source GROMACS Module for Automated Analysis of Nucleic Acid Secondary and Tertiary Structure in Molecular Dynamics Simulations www.biorxiv.org/content/10.64898/20…
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Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
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...
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Max-Planck-Gesellschaft @maxplanck.de · 09/09/2026
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
Call for independent Max Planck Research Groups
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 08/09/2026
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...
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Chris H. Hill @chillzaa.bsky.social · 24/08/2026
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
sciencedirect.com
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…
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Stephanie Wankowicz @stephanieaw.bsky.social · 11/08/2026
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.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 10/08/2026
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)
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CompBioPhys @compbiophys.bsky.social · 16/07/2026
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
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Alex Cope, PhD (he/him) @alexcope241.bsky.social · 08/07/2026
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...
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CompBioPhys @compbiophys.bsky.social · 19/06/2026
🎉 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...
nature.com
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...
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Alejandra Caraballo @esqueer.net · 10/06/2026
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.
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Haaris Ahsan Safdari @haarissafdari.bsky.social · 18/05/2026
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...
nature.com
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...
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Caroline Lynn Kamerlin ☀️ @lynnkamerlin.bsky.social · 01/06/2026
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.
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BioExcel CoE @bioexcelcoe.bsky.social · 29/05/2026
🎗️ Final reminder! This Sunday 31st May is the deadline: 💰 Early-bird registration 🗣️ Oral presentation abstract submission ➡️ bioexcel.eu/hzr0 #ComputerSimulation #conference #community
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 28/05/2026
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...
Stop sigh: “Speed bumps” for mitoribosomes: Mitoribosomes (white, with black outlines) do not produce mitochondrial membrane proteins at a constant rate. Instead, they slow down at specific points — molecular “speed bumps” — that help coordinate protein production, folding, and insertion into the inner mitochondrial membrane.
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Stephanie Wankowicz @stephanieaw.bsky.social · 21/05/2026
www.nature.com/articles/s41...
nature.com
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.
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Lorenz Lab @sonjalorenzlab.bsky.social · 14/05/2026
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...
jbc.org
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...
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Jan H. Jensen @janhjensen.bsky.social · 08/05/2026
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
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CompBioPhys @compbiophys.bsky.social · 04/05/2026
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
pubs.acs.org
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...
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Michal Kolář @mhko.bsky.social · 30/04/2026
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....
vscht.cz
Starting grants – Institutional Research Support - University of Chemistry and Technology, Prague
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Miro Astore @miroastore.bsky.social · 24/04/2026
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...
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Michal Kolář @mhko.bsky.social · 20/04/2026
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/...
academic.oup.com
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
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Amadeu Antonio Stiftung @amadeuantonio.bsky.social · 25/03/2026
#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. f.mtr.cool/zfvsjdkdak
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Chenggong惠成功 @chenggonghui.bsky.social · 30/03/2026
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...
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Elodie Carmen Leroy @ecleroy.bsky.social · 19/03/2026
🚨 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🧵)
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Michal Kolář @mhko.bsky.social · 12/03/2026
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.
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Neva Caliskan @caliskanlab.bsky.social · 06/03/2026
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
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Anders H. Lund @andershlund.bsky.social · 18/02/2026
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...
tinyurl.com
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
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 11/02/2026
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
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Marie Winz @mariewinz.bsky.social · 10/02/2026
#PhDPosition open — #RibosomeBiology & #Translation QC 📍 JGU Mainz, Germany 🗓️ Apply by 10 Mar 2026 (or until filled) 🔗 Full details + project options: 👉 ak-winz.pharmazie.uni-mainz.de/jobs/
ak-winz.pharmazie.uni-mainz.de
Jobs/internships/theses | Winz Lab - AK Winz
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CompBioPhys @compbiophys.bsky.social · 06/02/2026
🧐 You are a physicist or chemist who wants to reveal how life works at the molecular level? 🤓 You know how to combine computer power and theory to solve biological problems? ❤️ You just love doing science? 👉 Send us your application! 🔗 Current job adverts www.mpinat.mpg.de/grubmueller
Job advert for MD related research projects in the department of theoretical and computational biophysics @mpi-nat.bsky.social
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CompBioPhys @compbiophys.bsky.social · 28/01/2026
😲 #Deadline is approaching... Don't miss your chance to join the @bioexcelcoe.bsky.social #summer#school on #biomolecular #simulations in #sardinia 🇮🇹 @gromacs.bsky.social #pmx #hadddock #biobb
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Stand Up for Science! @standupforscience.net · 24/01/2026
This is Alex Pretti. This morning he was murdered by ICE. Six ICE agents held him down and shot him at point blank range. Alex was a nurse and researcher at the VA. Our thoughts are with his loved ones and we stand united in action calling for the abolishment of ICE. #ScientistsAgainstICE
Alex Pretti, wearing a green sweater with his VA badge on.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 22/01/2026
Did you miss our 2025 scientific lecture series at the Literaturherbst in Göttingen? Stream most German & English talks in full-length on our website💻. From baby talk to democracy and the vaccines of the future; there is something interesting for everybody! www.mpinat.mpg.de/4758909/media
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Caroline Lynn Kamerlin ☀️ @lynnkamerlin.bsky.social · 14/01/2026
Listen to this if you bear. Phone call from #Iran. I will transcript (pardon typos). "You cannot even imagine. Not even in your imaginations, what is happening in Iran. Thousands and thousands of people have been killed. 1/ www.instagram.com/reel/DTgIUBt...
instagram.com
omiddjalili on Instagram: "🚨Due to the regime cutting off the internet last 5 days messages coming out of Iran have decreased by 99% - this one made it throu…"
🚨Due to the regime cutting off the internet last 5 days messages coming out of Iran have decreased by 99% - this one made it through. The scale of civilian massacre is far beyond what has been reported. The figure of 12,000 killed is described as ‘almost a joke’ compared to the magnitude of the catastrophe that has taken place.The regime in Iran have carried out widespread and systematic deadly violence. “It is a massacre beyond human imagination”. There are subtitles so please go to the end. It is still happening. Please share widely.#IranianRevolution2026
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CompBioPhys @compbiophys.bsky.social · 13/01/2026
🎉 Now also published in @pubs.acs.org #Photonics ⏩ pubs.acs.org/doi/10.1021/... #MINFLUX #microscopy #Bayes
pubs.acs.org
Bayesian MINFLUX Localization Microscopy
MINFLUX microscopy allows for localization of fluorophores with nanometer precision by using targeted scanning with an illumination profile with a minimum. However, current scanning patterns and the o...
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Caroline Lynn Kamerlin ☀️ @lynnkamerlin.bsky.social · 12/01/2026
Over 100 hours of Internet and phone blackout, as the regime commits crimes against humanity. The death toll is now in the thousands. If you care *at all* about human rights, do something. Contact your representatives. Demand accountability. History will not forgive you for looking away. #Iran
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David Balchin @davidbalchin.bsky.social · 12/01/2026
If anyone is interested in making bacterial ribosome-nascent chain complexes and studying them using HDX-MS, we have written up a detailed protocol. rdcu.be/eYFx4 Characterise the conformational dynamics of the ribosome, nascent polypeptide and bound chaperones, label-free and at peptide-level
rdcu.be
Client Challenge
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Caroline Lynn Kamerlin ☀️ @lynnkamerlin.bsky.social · 11/01/2026
Iran has been under communications blackout for over 60 hours now. Several thousand people have been killed (numbers vary by source, I have seen between 2 and 5000 this morning). Iranians abroad don't know if their loved ones are alive or dead, have absolutely no way to communicate 1/
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Caroline Lynn Kamerlin ☀️ @lynnkamerlin.bsky.social · 09/01/2026
As a reminder, in the 2019 protests, the Iranian regime killed about 1500 people in less than two weeks. They do this under the cover of cutting internet. This time, they have cut off the internet, phone lines, and closed airspace. This is a crisis. Don't look away.
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MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 08/01/2026
📣 Talented PhD students wanted: The IMPRS for Genome Science @imprsgs.bsky.social and the DFG Research Training Group GönomiX are looking for you!
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Free Energy Workshop 2025 @feworkshop.bsky.social · 05/01/2026
Exciting news! We have a new website: omsf.io/alchemistry Your one-stop shop for everything related to our conference community. 🎉 BTW, registration is now open, so head over to secure your spot! We'll be sharing updates and details about the event. Bookmark it as there's plenty more to come!
omsf.io
Alchemistry Workshop in Free Energy Methods for Drug Design - Alchemistry
Annual conference on Free Energy Methods in Drug Discovery
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Chris H. Hill @chillzaa.bsky.social · 06/01/2026
🚨Last chance to apply for two PhD projects in my lab, applying structural biology and single molecule biophysics to investigate gene expression in RNA viruses: www.findaphd.com/phds/?Keywor...
findaphd.com
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CompBioPhys @compbiophys.bsky.social · 14/11/2025
👉Applications will be reviewed on a rolling basis until the #postodc or #phd #position is filled. 📩 Send us your message to explain why you are a great candidate to join the group "Computational Biomolecular Dynamics" of Bert de Groot @mpi-nat.bsky.social 🔗 www.mpinat.mpg.de/degroot #compbiophys
mpinat.mpg.de
Bert L. de Groot
The group studies the relationship between dynamics and function of biological macromolecules at the atomic level using computer simulations. Modern, sophisticated techniques are employed to follow the motions of atoms and molecules at timescales of femtoseconds to microseconds, thereby providing insight into the functional mechanism of e.g. enzymesand transport proteins. The main research focus lies on permeation events in membrane channels like aquaporins or gramicidin, collective and functionally essential modes of motion in enzymes, and the development of novel simulation techniques as an alternative to conventional simulation methods.
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Maria Niedernhuber @mariandrnh.bsky.social · 09/12/2025
anyone got any advice on the following situation? I wrote and did a big chunk of the admin for a large MRC grant which also also awarded. I am named in the Staff breakdown on the grant as "researcher co-lead" with 100%FTE, and I am mentioned by name as "postdoctoral researcher Maria Niedernhuber"
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Roberto Covino @rocovino.bsky.social · 05/12/2025
The Frankfurt Institute for Advanced Studies (FIAS) and the newly funded Cluster of Excellence SCALE are seeking several Independent Research Group Leaders to drive theoretical and computational research in molecular and cellular life science. fias.institute/de/das-fias/...
fias.institute
Independent Research Group Leaders (f/m/d) SCALE / FIAS
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Maksim Kalutskii @maksimkalutskii.bsky.social · 27/10/2025
📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...
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