Samuel Murail

The IBPC library was used as a location for the filming of a documentary about Marie Curie, entitled ‘Le journal intime de Marie Curie’ . It will be broadcast on Sunday 9 November on France 2's ‘13h15 Le Dimanche’ programme.
Trailer for the documentary:
www.instagram.com/reel/DQumf36...

Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events Molecular dynamics (MD) simulations are powerful tools for studying the movement and interactions of molecules, but they can be computationally expensive, especially for large biomolecules like proteins. This is problematic because accurately simulating the motions of these molecules is key to understanding their functions. Enhanced sampling methods, such as Simulated Tempering (ST), temperature Replica Exchange Molecular Dynamics (REMD), and Replica Exchange with Solute Tempering (REST and REST2), have been developed to overcome this challenge by improving the efficiency of MD simulations. This work presents a new enhanced sampling method called Simulated Solute Tempering 2 (SST2) that builds upon the strengths of ST and REST2. SST2 selectively scales the interactions inside a biomolecule and with its surrounding environment, effectively accelerating the exploration of its different structural states and their stabilities at various temperatures. SST2 is tested on three different systems (chignolin CLN025, Trp-Cage, and a protein–peptide complex, p97/PNGase) and is found to achieve comparable or superior sampling efficiency to ST, SST1, and REST2 while requiring fewer temperature rungs. Notably, SST2 is particularly well-suited for investigating large biomolecular systems, making it a valuable tool for studying a wide range of biomolecular processes, from protein folding to ligand binding.

🎉 Thrilled to announce that our paper "Simulated Solute Tempering 2 (SST2): An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events" is now published in JCTC! pubs.acs.org/doi/full/10....

Annonce_CPJ_Cnam | Nathalie Lagarde Un poste de Chaire de Professeur Junior (CPJ) est ouvert dans notre équipe de bioinformatique structurale appartenant au laboratoire GBCM du Conservatoire National des Arts et Métiers (Paris). 👉 Profi...

A junior chair professor position in computer science / chemoinformatics / structural bioinformatics is available in my former team in CNAM, Paris, France

Please contact Nathalie Lagarde for more details (nathalie.lagarde@lecnam.net)

CASP is no more.

Not unexpected, given the disastrous policy changes in the US, but nonetheless horrible news.

Exclusive: Famed protein structure competition nears end as NIH grant money runs out | Science | AAAS

I got fooled by AI-for-science hype—here's what it taught me I used AI in my plasma physics research and it didn’t go the way I expected.

Going to the hospital because I broke my wrist smashing the endorse button:
www.understandingai.org/p/i-got-fool...

The last version of SST2 manuscript is out. As recommended, we have performed additional simulations using the REST2 and SST1. SST2 offers highly competitive sampling efficiency, with significant advantages in terms of computational cost and ease of implementation compared to both REST2 and SST1.

After X’s repressive actions, hundreds of thousands in Turkey joined Bluesky, seeking a freer space. Reports of government censorship here are deeply troubling. Don’t squander this trust. This is a critical moment for principled leadership—not silent compromise. @jay.bsky.team

We are happy to announce the release of MassiveFold 1.5.0.

It is now possible to add post-translational modifications and to run ligand screening with AlphaFold3!

« J’ai entendu le président de la République dire qu’il faudrait rendre inéligible à vie ceux qui ont été condamnés pour corruption et fraude fiscale.

Ah bon ? Et pourquoi pas le reste ?

Pourquoi pas pour détournement de fonds publics ? »

— Marine Le Pen, le 5 avril 2013.

#PassionArchives

New preprint! @tatilab.bsky.social imaged the honeybee GABAA RDL receptor. ~10% of insecticides target insect GABAA receptors. She found a new allosteric modulation pocket, a PIP2 site, a closed avermectin-bound conformation, and maybe an unusual desensitized state.
www.biorxiv.org/content/10.1...

AlphaFold is running out of data — so drug firms are building their own version Nature - Thousands of 3D protein structures locked up in big-pharma vaults will be used to create a new AI tool that won’t be open to academics.

Thousands of 3D protein structures locked up in big-pharma vaults will be used to create a new AI tool that won’t be open to academics.
www.nature.com/artic...

Job alert ! I am looking for a postdoc to work on "computational investigation of ion-effects in ribozyme catalysis" to work with me in Paris (France). 1-year contract funded by @agencerecherche.bsky.social, with possible 2nd year in collab. with P. Jungwirth @iocbprague.bsky.social #compchem #RNA

GitHub - samuelmurail/af_analysis: Analysis of alphafold and colabfold results Analysis of alphafold and colabfold results. Contribute to samuelmurail/af_analysis development by creating an account on GitHub.

🔧 Install it easily with: "pip install af-analysis"
📂 Code: github.com/samuelmurail/af_analysis
📖 Documentation: af-analysis.readthedocs.io

🚀 Thrilled to share that our paper on af-analysis, a Python library for analyzing AlphaFold results, is now live on @joss-openjournals.bsky.social !
🔬✨ This open-source tool streamlines the analysis of protein structures, offering functions to compare, visualize, and evaluate model quality.

Just published in JOSS: 'Af-analysis: a Python package for Alphafold analysis' https://doi.org/10.21105/joss.07577

😂😂😂

Homme en costard entouré d'attributs des sciences dures (microscope, compas, pyramide), femme en jupe étroite et talons avec des attributs SHS (cahiers+globe), c'était peut-être pas indispensable de coller une illustration qui renforce les stéréotypes de genre +++ @lemonde.fr ?

Presented UDock and VTX today at Loria in Nancy, thanks Yasaman Karami and Ahmed Khakzad for the kind invitation!

🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...

correlation plot of experimental vs. predicted residence times, using Schrödinger's Unbinding Kinetics workflow

🌍 In the world of drug discovery, knowing a drug's residence time (τ) on its target can significantly impact its efficacy. Our new study presents innovative methods for predicting τ efficiently and accurately! 🧵🧵🧵

It is indeed striking how much AF3-based methods struggle to generalize to novel protein-ligand interfaces. It is also interesting that there remains a meaningful delta between AF3 and other reproductions at the most difficult generalization task (~25% vs ~13% success rate, so roughly double).

« Lettre à mes ravisseurs », par Nicolas Hénin : « Ma vengeance ultime est que le tribunal vous accorde tous les droits que vous m’avez reniés » TRIBUNE. « Votre cruauté n’a de comparable que celle des sbires de Bachar Al-Assad », affirme, dans une tribune au « Monde », l’ancien journaliste et ancien otage de l’organisation Etat islamique en S...

Il faut absolument lire, partager et méditer ce texte de @nicolashenin.net à quelques jours du procès de cinq de ses ravisseurs présumés en Syrie. Un exemple de dignité, d'humanité et de politique, de lucidité et de beauté. Merci infiniment, très cher confrère.
www.lemonde.fr/idees/articl...

Have protein-ligand co-folding methods moved beyond memorisation? Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!

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

🧵👇 (1/n)

Les arrondissements où la démographie baisse sont les 10e, 7e, 3e, 5e. Ceux où on ferme des classes sont les 18e, 19e et 20e.

1/3 des fermetures de classe concentrées sur 3 arrondissements populaires.

Foldseek-Multimer is a strategy for complex-to-complex protein structure alignment to quickly perform large-scale structural comparisons between complexes. @martinsteinegger.bsky.social

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

Cars CRS rue des écoles

12 camions de CRS pour 120 chercheurs et enseignants chercheurs devant le collège de France c'est émouvant de se sentir considérés 🥹

I’ve just done my #eXit! the X exodus is massive. Don't lose any of your followers. Thanks to #OpenPortability I've registered 252 new passengers for a journey to #BlueSky & #Mastodon. Join us on openportability.org and automatically find your communities on #January20!

Tech billionaires want to ‘overthrow democracy’ with social media, Spain PM Sánchez says “The technology that was intended to free us has become the tool of our own oppression.”

Tech billionaires want to ‘overthrow democracy’ with social media, Spain PM Sánchez says

“The technology that was intended to free us has become the tool of our own oppression.” www.politico.eu/article/spai...

Parcoursup est devenu une vitrine publicitaire pour le privé pendant que l’enseignement supérieur suffoque Au moment où s’ouvre Parcoursup, le sociologue des sciences et député LFI Arnaud Saint-Martin décrit dans cette tribune l’essor du « business honteux » de l’enseignement supérieur privé. Et pointe la ...

Parcoursup est devenu une vitrine publicitaire pour le privé pendant que l’enseignement supérieur suffoque www.nouvelobs.com/opinions/202...

La motion de défiance après l'annonce par la bureaucratie du CNRS du définancement de trois quarts des laboratoires, préambule au démantèlement du CNRS, monte gentiment, à 500 signatures/jour.
framaforms.org/motion-de-de...