🎗️ reminder that our #webinar on "Mastering the Accelerated Weight Histogram method" will take place next week;

🗓️ 10 February 2026, 15:00 CET
✍️ bioexcel.eu/5t76

#moleculardynamics

🗓️ Save the Date!
The 5th European RosettaCon – Crossing Boundaries with Protein Design will take place in Lisbon, Portugal 🇵🇹
🗓️ October 28–30, 2026
Join the protein design community for an inspiring scientific meeting at the intersection of innovation and design.

Ab initio prediction of RNA structure ensembles with RNAnneal

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Ab initio prediction of RNA structure ensembles with RNAnneal [new]
...leverages generative deep learning with statistical physics and MD to determine 3D structural ensembles from primary sequences, aiding design.

Undergraduates Rosetta Commons Research Experience for Undergraduates (REU) AI for Biomolecular Structure Prediction and Design Interns in this geographically-distributed REU program participate in research using…

Final stretch to apply for undergraduate summer internships in the Rosetta Commons! Come design proteins, develop AI and physics-based methods to model biomolecules, and impact health, materials, and sustainability! Application deadline is Sunday Feb 1.
rosettacommons.org/education/reu/

Spotlight on the Shingles Vaccine—Again! Two new studies add to a remarkable body of evidence for benefit

Excellent overview of the (mind-blowing) effects of the Shingles vaccine against dementia by @erictopol.bsky.social Ground Truth 🧪 "Two new studies add to a remarkable body of evidence for benefit" ⬇️

open.substack.com/pub/erictopo...

"While the concept of condensates is successfully rewriting cell biology textbooks, there is some danger of overhype and backlash."

This workshop summary is great - particularly the idea to shift from "Is it a condensate?" to "what problem does that solve?"

but "successfully" stood out for me here

Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n

Experimental structures provide valuable hypotheses and accelerate but do not replace evolutionary and statistical analyses of protein sequences

Rate your score on Factor Fexcectorn.

Well done, Scientific Reports. pubpeer.com/publications...

The official home of the Python Programming Language

TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵

Join our lab dibernardo.tigem.it for the #ERC-funded project DIMERCIRCUITS at @tigem.bsky.social. We are building synthetic gene circuits to power next-generation gene and cell therapies. We are looking for candidates with a PhD in #SyntheticBiology or related. Apply by email: dibernardo@tigem.it

🚀 Launch your career in advanced gene and cell therapies! 🚀

RAREFIND #MSCA-COFUND #PhD Programme opens its call for applications!

👉Know more and apply now: www.rarefind-cofund.eu

#RAREFINDPhD

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.

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

We are hiring a Bioinformatician expert in NGS for our Bioinformatics Core @tigem.bsky.social please share with anyone that may be interested.

Very nice presentation of @eriklindahl.bsky.social about his work to integrate AI, MD and experiments. 🤩 #EBSA2025

Are you curious about ligand selectivity and modulation mechanisms of the voltage-gated potassium channel Kv7 family? Stop by Poster #39!

#EBSA2025 #IonChannels #StructuralBiology #ComputationalBiophysics

Excited to be at #EBSA2025!
Today I'll present my postdoc project carried out under the supervision of @delemottelab.bsky.social and with the collaboration of Sara Liin and her amazing team!

🌍 Attending #ASGCT2025 in #NewOrleans?
Don’t miss this Scientific Symposium hosted by the Coalition of International Gene Therapy Societies:

📌 Clinical Trials Around the Globe
🗓️ [Today, May 16th]
🕗 8:00 AM – 9:45 AM
📍 Room 293–296

#GeneTherapy #ASGCT #AAV #Retina #LiverGeneTherapy #RareDisease

Gene therapy in children with AIPL1-associated severe retinal dystrophy: an open-label, first-in-human interventional study Our findings indicate that young children with AIPL1-related retinal dystrophy benefited substantially from subretinal administration of rAAV8.hRKp.AIPL1, with improved visual acuity and functional vi...

A new paper hitting the press: Gene therapy for AIPL-1 retinal dystrophy. Almost all kids with this can only perceive light, at best. Getting early will help with vision also neurodevelopment and psychosocial aspects. 🧬 ⭐ 👁

www.thelancet.com/journals/lan...

Structures of protein folding intermediates on the ribosome The ribosome biases the conformations sampled by nascent polypeptide chains along folding pathways towards biologically active states. A hallmark of the co-translational folding (coTF) of many protein...

Preprint! All-atom structures of 2 folding intermediates on the ribosome, along parallel pathways & conserved across Ig domains, by 19F NMR & MD

Co-led by @julianstreit.bsky.social, & thanks twlodarski.bsky.social, Alki, Lisa & John Christodoulou!

#nmrchat #compbio
www.biorxiv.org/content/10.1...

BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design by @yehlincho.bsky.social @martinpacesa.bsky.social @sokrypton.org 🧶🧬

www.biorxiv.org/content/10.1...

Fig 3d Scatterplots compare xT-Fold predictions (x axis) to other models (y axis), color coded by perplexity (green for high, purple for low).

Yet another PLM, this one with 100B params, that fails to outperform AF2 (93M params) when MSAs are provided www.nature.com/articles/s41...

We are recruiting a colleague to our division at Chalmers in Data-Driven Life Science (broadly defined), a competitive starting package is offered and you get to be part of a support, yet young and ambitious research environment. Apply here: www.chalmers.se/en/about-cha...

Honored to be part of @tigem.bsky.social and Fondazione Telethon

Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding A major challenge for many rare-event sampling strategies is the identification of progress coordinates that capture the slowest relevant motions. Machine-learning methods that can identify progress coordinates in an unsupervised manner have therefore been of great interest to the simulation community. Here, we developed a general method for identifying progress coordinates “on-the-fly” during weighted ensemble (WE) rare-event sampling via deep learning (DL) of outliers among sampled conformations. Our method identifies outliers in a latent space model of the system’s sampled conformations that is periodically trained using a convolutional variational autoencoder. As a proof of principle, we applied our DL-enhanced WE method to simulate the NTL9 protein folding process. To enable rapid tests, our simulations propagated discrete-state synthetic molecular dynamics trajectories using a generative, fine-grained Markov state model. Results revealed that our on-the-fly DL of outliers enhanced the efficiency of WE by >3-fold in estimating the folding rate constant. Our efforts are a significant step forward in the unsupervised learning of slow coordinates during rare event sampling.

Leung et al. used deep autoencoders with outlier detection to guide weighted ensemble simulations of NTL9 folding, achieving up to threefold better efficiency than standard methods. pubs.acs.org/doi/full/10....

The Protein Design Archive (PDA): insights from 40 years of protein design - Nature Biotechnology Nature Biotechnology - The Protein Design Archive (PDA): insights from 40 years of protein design

Chronowska et al. introduce the Protein Design Archive, a curated database of over 1,500 de novo designs, revealing rapid growth from rational to deep learning–based methods. Their website offers key metrics and filtering tools for guiding future designs. www.nature.com/articles/s41...

In Brief: A potential first-in-class treatment using @boehringerglobal.bsky.social's lentivirus-based CFTR gene addition therapy for cystic fibrosis begins clinical trials www.nature.com/articles/s41...
rdcu.be/eecLO

🚨 The latest study from #NatureCommunications, led by Pasquale Piccolo, systematically evaluated AAV-mediated liver transduction across different fibrosis models.

🚀 PhD Opportunity – NC-mTORC1 & Genetic Diseases!

Join @tigem.bsky.social & Univ. of Naples to explore Non-Canonical mTORC1 signaling in mTORopathies like BHD & TSC!

🚀 Our mission 🧬

Our mission is to push scientific boundaries through cutting-edge research, innovative therapies, and training the next generation of biomedical experts.
Learn more: www.tigem.it
✨ #Genetics #RareDiseases #MedicalResearch