Julie Ledoux
@jldx.bsky.social
Postdoctoral researcher in computational structural biology @ Laboratory of Theoretical Biochemistry, Paris.
For more on how to talk about tech sold as "AI" in more precise terms: buttondown.com/maiht3k/arch...
How to talk about
Emily M. Bender and Nanna Inie In our op-ed for Tech Policy Press ("We Need to Talk About How We Talk About 'AI'"), we made the case against the...
buttondown.com
When utilized in literature review, LLMs consistently 1. fail to mention female authors in female-led literatures, 2. insist that men are more influential or more heavily cited when this is contradicted by objective citation counts, and 3. attribute women’s work to hallucinated male scholars.
Congratulations to Bjarne Feddersen for his work on benchmarking umbrella sampling workflows for PMF calculations of membrane permeation! Systematic work that provides guidance on how to approach these to minimise compute resource. @oxfordbiochemistry.bsky.social. pubs.acs.org/doi/10.1021/...
Umbrella Sampling Workflows for Fast-Converging PMF Calculations without Artificial WHAM Constraints
Umbrella sampling is a powerful tool to investigate the underlying free-energy landscapes that govern the permeation properties of small molecules through complex lipid bilayers. However, obtaining co...
pubs.acs.org
Role of Water Models in Simulations of Ion Conduction in Potassium Channels https://www.biorxiv.org/content/10.1101/2025.10.24.684299v1
GROMODEX: Optimisation of GROMACS Performance through a Design of Experiment Approach https://www.biorxiv.org/content/10.1101/2025.10.08.681202v1
Integrating the MARTINI2 Coarse-Grained Force Field into HADDOCK3 for Faster Modelling of Large Biomolecular Complexes https://www.biorxiv.org/content/10.64898/2026.04.25.720800v1
So it is out! 🎉 I am so excited to share our preprint with Fabio Sterpne and @baam93.bsky.social on the development of a force field for oligourea foldamers, new self-assembling polymers of unnatural amino acids, designed for water desalination membranes. www.biorxiv.org/content/10.6...
biorxiv.org
Biochemist Elizabeth Bugie co-discovered streptomycin (with Selman Waksman), the first antibiotic against Mycobacterium tuberculosis. Waksman went on to win the 1952 Nobel Prize for Medicine & took full credit for the discovery. Bugie died #OTD in 2001. #WomenInSTEM #MatildaEffect (1/2)
On this 1st April I'm happy to release a technical report from our startup MirageBio, describing a new protein structure model with state-of-the-art performance. jgreener64.github.io/posts/techni...
MirageBio technical report
jgreener64.github.io
Use the AI-Powered 3D Structure Similarity Search This new RCSB PDB feature delivers faster and more scalable structural comparisons across experimentally determined and predicted Computed Structure Models (CSMs).
Use the AI-Powered 3D Structure Similarity Search
This new feature delivers faster and more scalable structural comparisons across experimentally determined and predicted Computed Structure Models (CSMs).
rcsb.org
L'évènement #ReCombinaisons est de retour à @pasteur.fr en 2026 avec un programme alléchant ! (On y retrouvera notamment @jeanneadebats.bsky.social et @audreypleynet.bsky.social !)
@sdvupsaclay.bsky.social · 5mo agoReCombinaisons - Institut Pasteur, 10 et 11 avril 2026
Book review 📚 These women helped to shape quantum mechanics — it’s time to recognize them go.nature.com/3Ls2yYu
These women helped to shape quantum mechanics — it’s time to recognize them
An astute book redresses our collective perception of a field that became known as ‘boys’ physics’.
go.nature.com
The chance encounter of an economist, a pathologist and physicist resulted in a highly multidisciplinary study that used an epidemiological model to trace the spread of rumors in the early days of the French Revolution. I had the chance to cover this fascinating research for @nature.com
An abiding mystery of the French Revolution is solved — by epidemiology
The period of panic and unrest called the Great Fear was triggered by deliberately spread rumours, according to methods borrowed from pandemic playbooks.
nature.com
I LIVE for catchy methods names and funny conference presentation titles
Dr. Hab Sophie Sacquin-Mora@sacquin-mo.eurosky.social · last yr.Jonathan Essex opens the modelling session at #EBSA2025 by discussing the CARBONARA model, wich ist on spot for an italian meeting.
Studies point to several reasons why fewer women than men are submitting their work https://go.nature.com/3HlUFS8
Gender equality in research publishing is a responsibility for everyone
A concerted effort is needed to support women in their choice of journal when submitting their manuscript.
go.nature.com
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!
Et voilà, les plus grands spécialistes de tout, les fameux toutologues, commencent à annoncer que l'on a trouvé du phytoplancton intersidéral.... Nous, scientifiques, devons faire attention à notre manière de communiquer. Ce n'est pas le moment de perdre la confiance des citoyens !
If you want to know how to fight bacterial resistance @france.theconversation.com Pour comprendre comment contrer la résistance bactérienne @france.theconversation.com @barbault.bsky.social @upcite.bsky.social @ctm-itodys.bsky.social @itodys.bsky.social theconversation.com/resistance-b...
Résistance bactérienne aux antibiotiques : mieux la comprendre et mieux la contrer
En comprenant comment les bactéries résistent aux antibiotiques, on pourrait inventer de nouvelles méthodes pour améliorer les traitements des infections.
theconversation.com
Given discussions at I had at #ESCMIDGlobal, it might be useful for new researchers to know how a journal editor screens submissions (obviously this is my approach and so it might differ for others).
We (@sacquin-mo.bsky.social, Chantal Prevost and I) teamed up with @etiennereboul.bsky.social and @ataly.bsky.social to design a parallelized MDAKit implementation of the Proteic Menger Curvatures. Local protein dynamics and backbone flexibility have never been easier and faster to compute 😁
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.Menger_Curvature : a MDAKit implementation to decipher the dynamics, curvatures and flexibilities of polymeric backbones at the residue level https://www.biorxiv.org/content/10.1101/2025.04.04.647214v1
Research suggests that contrary to scientists' worries, there is no reputational penalty for shared first authorships, even for the person named second ― at least under experimental conditions1. https://go.nature.com/4c46IPm
Does sharing first authorship on a paper carry a penalty? What the research says
Study dispels myth that order of names in a paper’s author list dictates perception of success.
go.nature.com
You can download my protein structure-inspired artwork from pdb webpage: pdb101.rcsb.org/sci-art/bezs... @rcsbpdb.bsky.social @pdbeurope.bsky.social #sciart
PDB101: Irina Bezsonova Gallery
PDB-101: Training, Outreach, and Education portal of RCSB PDB
pdb101.rcsb.org
Academia’s often misguided view is that resilience is the ability to adapt and overcome challenges or adversity, but such an attitude can mask a toxic lab culture, say some researchers. https://go.nature.com/4kv5ro4
‘I was told to toughen up’: is academia getting resilience all wrong?
Being repeatedly told to bounce back and develop a thicker skin can mask a toxic lab culture.
go.nature.com
