How can we identify cryptic binding sites that are not visible in the structure of a protein in its ground state? 🧐 In our new Sci Adv paper, we used ML and fine-tuned a Protein language model to identify and predict these cryptic sites directly from sequences. www.science.org/doi/10.1126/...

CryptoBank: A resource for the identification and prediction of cryptic sites in proteins

CryptoBank reveals and predicts cryptic sites from protein sequence to guide drug discovery.

science.org

"Cancel ChatGPT" goes mainstream after Sam Altman takes the U.S. department of war deal Anthropic refused — in surveillance of U.S. citizens and autonomous weapons. www.windowscentral.com/artificial-i... #chatgpt #openai #samaltman #apocalypse

"Cancel ChatGPT" movement goes big after OpenAI's latest move

After Anthropic refused flat out to agree to apply Claude AI to autonomous weapons and mass surveillance of American citizens, OpenAI jumps right into bed with the United States Department of War.

windowscentral.com

Wonderful support from Pauline Juyoux and Guy Schoehn IBS Grenoble on the amazing new CM02 microscope, @gervasiolab.bsky.social for wonderful MD studies!

Then HR-HAIR from @olibclarke.bsky.social really improved our reconstructions www.biorxiv.org/content/10.1...

HexAufoil grids from Chris Russo's group @mrclmb.bsky.social gave amazing results for this 86 kDa complex!

New Preprint alert! Excited to share our latest work on the #MAPKinases from stellar PhD student Jill von Velsen. First structures of the MAP2K MEK1 activating its substrate MAPK between 2.9 and 3.6A - amazing resolutions for such a small and mobile complex! www.biorxiv.org/content/10.6...

Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42... To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology

Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...

nature.com

I fully endorse this. Political leaders are falling prey to AI hype, and seem to lack any kind of help from reputable sources who could counter the false claims of tech CEOs. Where are their science advisers???

Kris Shrishak@krisshrishak.bsky.social · 10mo ago

In a short piece for @techpolicypress.bsky.social, @abeba.bsky.social and I write #AIHype Is Steering EU Policy Off Course. Stop peddling in unscientific discourse about “AGI” and “superintelligence.” Serve citizens. Don't cater to the whims of tech CEOs. www.techpolicy.press/ai-hype-is-s...

How do proteins really fold? Our latest @pubs.acs.org JPCL paper with @saureli.bsky.social @valeriorizzi.bsky.social @mheritier.bsky.social unveils a new MD strategy to investigate it in atomistic resolution by focusing on water and side-chain interactions. check it out pubs.acs.org/doi/10.1021/...

The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables

Protein folding remains a formidable challenge despite significant advances, particularly in sequence-to-structure prediction. Accurately capturing thermodynamics and intermediates via simulations dem...

pubs.acs.org

New in @pubs.acs.org JCTC: We've mapped the complete activation pathway of the β1-adrenergic receptor using our OneOPES enhanced sampling method and tailored CVs. Our approach reveals how sodium ions, water networks & protein microswitches work together. pubs.acs.org/doi/full/10.... #GPCR

Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation

The beta-1 adrenergic receptor (ADRB1) is a critical target for cardiovascular drugs, yet our understanding of how it is activated remains incomplete. Capturing the concerted interplay of agonists, solvent, ions, and protein microswitches is a significant challenge for conventional simulation methods and is essential for unraveling this process. Here, we address this challenge by implementing a powerful enhanced sampling framework that integrates the OneOPES enhanced sampling algorithm with a set of biologically motivated collective variables (CVs). These CVs are designed to track several key features of the activation process simultaneously, including rearrangement of conserved microswitches, the state of the sodium ion binding pocket, and dynamics of critical water molecules. Using this framework, we mapped the multidimensional free energy landscapes of the ADRB1 receptor in both its apo- and adrenaline-bound holo states. Our analysis reveals a detailed, stepwise activation pathway that quantifies the known modulatory roles of sodium ions and protonation states and identifies essential water-mediated networks that stabilize the active conformation. This work provides a detailed overview of ADRB1 activation and establishes the robustness of our OneOPES approach for investigating complex activation mechanisms with the potential for application to other Class A GPCRs.

pubs.acs.org

Happy to share the latest work from the lab, led by @mudgal17.bsky.social‬, in collaboration with the Weis lab @ethzurich.bsky.social. How do nuclear membranes fuse during NPC assembly? We answer this question in our latest work, where we identify a new mechanism for membrane fusion… (1/13)

bioRxiv Cell Biology@biorxiv-cellbio.bsky.social · last yr.

A conserved mechanism of membrane fusion in nuclear pore complex assembly https://www.biorxiv.org/content/10.1101/2025.07.21.665908v1

AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done. clauswilke.substack.com/p/no-alphafo...

No, AlphaFold has not completely solved protein folding

Biology is hard. Yes, even for AI.

clauswilke.substack.com

“the 1.1 million international students studying in the US contributed $43.8bn to the US economy during the 2023–2024 academic year, creating 378,175 jobs nationwide.” www.aljazeera.com/news/2025/6/...

Can the US afford to lose its 1.1 million international students?

International students contributed $43.8bn to the US economy last year and created 378,175 jobs nationwide.

aljazeera.com

Great to see our collaborative work featured by @irbbarcelona.org! ➡️ Read more here: bit.ly/42LlJm9 📑 Read the full article: rdcu.be/ef6YX 📝 Support our statement: bit.ly/3zVS3qm #MDDB #FAIRdata #OpenScience #MolecularDynamics

IRB Barcelona@irbbarcelona.org · last yr.

Más de 100 expertos, coordinados desde el #IRBBarcelona, reclaman que los datos en simulación molecular se ajusten a los principios 'Fair': accesibles, interoperables, fáciles de encontrar y reutilizables. 📰 @lavanguardia.com  🔗 https://f.mtr.cool/ncjierxuzt #IRBScience #MolecularSimulation 🧪

Force fields with QM accuracy and MM speed are the theoretical biophysicist's Philosopher's Stone. I used ANIX2 with OpenFF and OpenMM. The results were insightful but at the expense of huge computational costs. #MLFF #biophysics #moleculardynamics

On the design space between molecular mechanics and machine learning force fields

A force field as accurate as quantum mechanics (QMs) and as fast as molecular mechanics (MMs), with which one can simulate a biomolecular system efficiently eno

pubs.aip.org

Andrew Chen, co-founder of one of my favorite denim brands, 3sixteen, breaks down how the tariffs affect his company IG 3sixteen

…and @alfonsovalencia.bsky.social advocates in @emboreports.org for a distributed biomedical database infrastructure based on the imperiled yet utterly essential CDC resources www.embopress.org/doi/10.1038/...

Decentralized databases in biomedical research: lessons from recent events: The recent shutdown of critical health databases by the US CDC is a wake-up call for the research community about the vulnerability of centralised databases: EMBO reports: Vol 0, No 0

EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.

embopress.org

Very proud of our new review article on the Beta 1-Adrenergic GPCR now available on bioRxiv: www.biorxiv.org/content/10.1.... With @saureli.bsky.social @valeriorizzi.bsky.social and Nicola we used OneOPES to fully converge the free energy landscapes associated with B1AR apo/holo activation.

EMBL has a single PhD application where a student can apply to any of our 80 labs in our 6 sites, with applications twice a year--the next March 10th! No need for MS, no application fee. Ranked 13th in the world on basis of publications, with emphais on junior faculty www.embl.org/about/info/e...

Since US President Donald Trump took office last month, his team has made major changes that have disrupted research and research institutions in the US and beyond. Follow our coverage of the Trump administration's impact on science around the world: https://go.nature.com/3QGKmJu

How Trump 2.0 is reshaping science

Since US President Donald Trump took office in January 2025, his team has made major changes to the federal government that have disrupted research and ...

go.nature.com

Awesome paper! BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1... Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

Our new review article on "Computational advances in discovering cryptic pockets for drug discovery" is now available on COSB doi.org/10.1016/j.sb... In collaboration with Pande's lab at JnJ and Cournia's lab at BRFAA we reviewed the state of the art in silico tools for studying cryptic pockets.

We are searching for a Research Assistant/Bioinformatician at @irbbarcelona.org bbglab.irbbarcelona.org/2024/12/job-... #IRBJobs

pubmed.ncbi.nlm.nih.gov/39643640/ “while AlphaFold3 shows improved performance over AlphaFold2 in predicting overall GPCR backbone architecture, significant discrepancies persist in ligand-binding poses, particularly for ions, peptides, and proteins.”

AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors - PubMed

G protein-coupled receptors (GPCRs) are critical drug targets involved in numerous physiological processes, yet many of their structures remain unresolved due to inherent flexibility and diverse ligan...

pubmed.ncbi.nlm.nih.gov

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

I'm excited to share a new manuscript with Jiaqi Zhu characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs: biorxiv.org/content/10.1... Code + Ensembles: github.com/paulrobustel...

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org

PLUMED Tutorials: a collaborative, community-driven learning ecosystem

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...

arxiv.org

Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hr

Hello! I'm posting this both here and on the X-rated site, let's see where it gets more re-posts 😇. We are looking for a research software engineer to help us develop (even) better code for #compchem #atomicscale #machinelearning. Check out the specs and apply! www.epfl.ch/labs/cosmo/i...

Jobs

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epfl.ch

Very excited to present the structural and mechanistic basis for stress response silencing by the monster E3 ligase SIFI. www.biorxiv.org/content/10.1...