Samuel Murail
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samuelmurail.bsky.social
Samuel Murail
@samuelmurail.bsky.social
Associate Professor @upcite.bsky.social. Molecular Modeller of Peptide & Membrane Proteins.
Pinned
🎉 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....
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.
pubs.acs.org
Reposted by Samuel Murail
Elena Mistrello. Dessinatrice italienne expulsée de France pour « menace grave pour l’ordre public »

➡️ https://l.humanite.fr/nqu
November 24, 2025 at 5:15 PM
Reposted by Samuel Murail
A few py2Dmol updates 🧬

py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
Reposted by 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...
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November 7, 2025 at 1:17 PM
🎉 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....
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.
pubs.acs.org
October 27, 2025 at 9:31 AM
Reposted by Samuel Murail
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 ([email protected])
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...
www.linkedin.com
September 24, 2025 at 7:59 AM
Reposted by Samuel Murail
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
Exclusive: Famed protein structure competition nears end as NIH grant money runs out
Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold
www.science.org
July 4, 2025 at 11:29 AM
Reposted by Samuel Murail
Going to the hospital because I broke my wrist smashing the endorse button:
www.understandingai.org/p/i-got-fool...
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.
www.understandingai.org
May 19, 2025 at 6:04 PM
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.
Simulated Solute Tempering 2 [updated]
Accelerates biomolecule simulations by scaling solute interactions, enhancing structural sampling at fewer temperatures.
May 9, 2025 at 12:38 PM
Reposted by Samuel Murail
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
April 16, 2025 at 12:14 AM
Reposted by Samuel Murail
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!
April 11, 2025 at 10:02 AM
Reposted by Samuel Murail
« 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
March 31, 2025 at 2:21 PM
Reposted by Samuel Murail
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...
March 27, 2025 at 7:51 AM
Reposted by Samuel Murail
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...
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.
www.nature.com
March 27, 2025 at 8:51 PM
Reposted by Samuel Murail
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
March 26, 2025 at 8:48 AM
🚀 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
March 14, 2025 at 8:49 AM
Reposted by Samuel Murail
Just published in JOSS: 'Af-analysis: a Python package for Alphafold analysis' https://doi.org/10.21105/joss.07577
March 14, 2025 at 8:16 AM
Reposted by Samuel Murail
😂😂😂
March 6, 2025 at 6:34 PM
Reposted by Samuel Murail
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 ?
March 4, 2025 at 2:35 PM
Reposted by Samuel Murail
Presented UDock and VTX today at Loria in Nancy, thanks Yasaman Karami and Ahmed Khakzad for the kind invitation!
February 28, 2025 at 2:45 PM
Reposted by Samuel Murail
🚀 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...
February 17, 2025 at 6:56 AM
Reposted by Samuel Murail
🌍 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! 🧵🧵🧵
February 14, 2025 at 3:40 AM
Reposted by Samuel Murail
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).
In this work, we explored how training data similarity impacts protein-ligand prediction accuracy—an overlooked aspect in recent benchmarks. Our analysis shows that the current co-folding methods struggle to generalize beyond ligand poses in their training data.(2/n)
February 8, 2025 at 2:08 PM
Reposted by Samuel Murail
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...
« 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...
www.lemonde.fr
February 10, 2025 at 6:14 PM
Reposted by Samuel Murail
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)
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...
www.biorxiv.org
February 8, 2025 at 10:02 AM
Reposted by Samuel Murail
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.
February 7, 2025 at 1:19 PM