Samuel Murail
@samuelmurail.bsky.social
đ€ 93
đ„ 184
đ 8
Associate Professor
@upcite.bsky.social
. Molecular Modeller of Peptide & Membrane Proteins.
pinned post!
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.
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5 months ago
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Matthieu Montes
9 days ago
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]
)
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Annonce_CPJ_Cnam | Nathalie Lagarde
Un poste de Chaire de Professeur Junior (CPJ) est ouvert dans notre Ă©quipe de bioinformatique structurale appartenant au laboratoire GBCM du Conservatoire National des Arts et MĂ©tiers (Paris). đ Profi...
https://www.linkedin.com/posts/nathalie-lagarde-9b5429225_annoncecpjcnam-activity-7376514827952865280-1szd?utm_source=share&utm_medium=member_android&rcm=ACoAAAP5NAgBj9ADjeuPgEB9u4rFwCUCUw6wJdQ
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Marc Lensink
3 months ago
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
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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
https://www.science.org/content/article/exclusive-famed-protein-structure-competition-nears-end-nih-grant-money-runs-out
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Eugene Vinitsky đ
5 months ago
Going to the hospital because I broke my wrist smashing the endorse button:
www.understandingai.org/p/i-got-fool...
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I got fooled by AI-for-science hypeâhere's what it taught me
I used AI in my plasma physics research and it didnât go the way I expected.
https://www.understandingai.org/p/i-got-fooled-by-ai-for-science-hypeheres
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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.
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5 months ago
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AltuÄ ĂztĂŒrk
6 months ago
After Xâs repressive actions, hundreds of thousands in Turkey joined Bluesky, seeking a freer space. Reports of government censorship here are deeply troubling. Donât squander this trust. This is a critical moment for principled leadershipânot silent compromise.
@jay.bsky.team
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Marc Lensink
6 months ago
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!
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Antton Rouget
6 months ago
« Jâai entendu le prĂ©sident de la RĂ©publique dire quâil faudrait rendre inĂ©ligible Ă vie ceux qui ont Ă©tĂ© condamnĂ©s pour corruption et fraude fiscale. Ah bon ? Et pourquoi pas le reste ? Pourquoi pas pour dĂ©tournement de fonds publics ? » â Marine Le Pen, le 5 avril 2013.
#PassionArchives
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Hugues Nury
6 months ago
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...
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RCSB Protein Data Bank
6 months ago
Thousands of 3D protein structures locked up in big-pharma vaults will be used to create a new AI tool that wonât be open to academics.
www.nature.com/artic...
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AlphaFold is running out of data â 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 wonât be open to academics.
https://www.nature.com/articles/d41586-025-00868-9
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Ălise DubouĂ©-Dijon
6 months ago
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
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đ Thrilled to share that our paper on af-analysis, a Python library for analyzing AlphaFold results, is now live on
@joss-openjournals.bsky.social
! đŹâš This open-source tool streamlines the analysis of protein structures, offering functions to compare, visualize, and evaluate model quality.
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7 months ago
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Journal of Open Source Software
7 months ago
Just published in JOSS: 'Af-analysis: a Python package for Alphafold analysis'
https://doi.org/10.21105/joss.07577
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Tommy Byrne
7 months ago
đđđ
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Dr. Hab Sophie Sacquin-Mora
7 months ago
Homme en costard entourĂ© d'attributs des sciences dures (microscope, compas, pyramide), femme en jupe Ă©troite et talons avec des attributs SHS (cahiers+globe), c'Ă©tait peut-ĂȘtre pas indispensable de coller une illustration qui renforce les stĂ©rĂ©otypes de genre +++
@lemonde.fr
?
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Matthieu Montes
7 months ago
Presented UDock and VTX today at Loria in Nancy, thanks Yasaman Karami and Ahmed Khakzad for the kind invitation!
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Rafael C. Bernardi
8 months ago
đ First Bluesky Post! đ VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 yearsânew 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...
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Dima Lupyan
8 months ago
đ In the world of drug discovery, knowing a drug's residence time (Ï) on its target can significantly impact its efficacy. Our new study presents innovative methods for predicting Ï efficiently and accurately! đ§”đ§”đ§”
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Mohammed AlQuraishi
8 months ago
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).
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Edwy Plenel
8 months ago
Il faut absolument lire, partager et méditer ce texte de
@nicolashenin.net
à quelques jours du procÚs de cinq de ses ravisseurs présumés en Syrie. Un exemple de dignité, d'humanité et de politique, de lucidité et de beauté. Merci infiniment, trÚs cher confrÚre.
www.lemonde.fr/idees/articl...
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« Lettre Ă mes ravisseurs », par Nicolas HĂ©nin : « Ma vengeance ultime est que le tribunal vous accorde tous les droits que vous mâavez reniĂ©s »
TRIBUNE. « Votre cruautĂ© nâa de comparable que celle des sbires de Bachar Al-Assad », affirme, dans une tribune au « Monde », lâancien journaliste et ancien otage de lâorganisation Etat islamique en S...
https://www.lemonde.fr/idees/article/2025/02/10/lettre-a-mes-ravisseurs-par-nicolas-henin-ma-vengeance-ultime-est-que-le-tribunal-vous-accorde-tous-les-droits-que-vous-m-avez-renies_6540408_3232.html
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Peter Ć krinjar
8 months ago
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 đčRuns Nâ Posesđč!
www.biorxiv.org/content/10.1...
đ§”đ (1/n)
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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...
https://www.biorxiv.org/content/10.1101/2025.02.03.636309v1
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FX Coudert
8 months ago
Les arrondissements oĂč la dĂ©mographie baisse sont les 10e, 7e, 3e, 5e. Ceux oĂč on ferme des classes sont les 18e, 19e et 20e. 1/3 des fermetures de classe concentrĂ©es sur 3 arrondissements populaires.
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Nature Methods
8 months ago
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...
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Kevin Cariou
8 months ago
12 camions de CRS pour 120 chercheurs et enseignants chercheurs devant le collĂšge de France c'est Ă©mouvant de se sentir considĂ©rĂ©s đ„č
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Iâve 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
!
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OpenPortability
Libérez vos espaces numériques
https://openportability.org
8 months ago
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WaterBluSky đșđž đ» đșđŠ
8 months ago
Tech billionaires want to âoverthrow democracyâ with social media, Spain PM SĂĄnchez says âThe technology that was intended to free us has become the tool of our own oppression.â
www.politico.eu/article/spai...
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Tech billionaires want to âoverthrow democracyâ with social media, Spain PM SĂĄnchez says
âThe technology that was intended to free us has become the tool of our own oppression.â
https://www.politico.eu/article/spain-pedro-sanchez-big-tech-billionaires-democracy-social-media/
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Mona Chollet
9 months ago
Parcoursup est devenu une vitrine publicitaire pour le privĂ© pendant que lâenseignement supĂ©rieur suffoque
www.nouvelobs.com/opinions/202...
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Parcoursup est devenu une vitrine publicitaire pour le privĂ© pendant que lâenseignement supĂ©rieur suffoque
Au moment oĂč sâouvre Parcoursup, le sociologue des sciences et dĂ©putĂ© LFI Arnaud Saint-Martin dĂ©crit dans cette tribune lâessor du « business honteux » de lâenseignement supĂ©rieur privĂ©. Et pointe la ...
https://www.nouvelobs.com/opinions/20250118.OBS99142/parcoursup-est-devenu-une-vitrine-publicitaire-pour-le-prive-pendant-que-l-enseignement-superieur-suffoque.html
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Pr. Logos
9 months ago
La motion de défiance aprÚs l'annonce par la bureaucratie du CNRS du définancement de trois quarts des laboratoires, préambule au démantÚlement du CNRS, monte gentiment, à 500 signatures/jour.
framaforms.org/motion-de-de...
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Syma Khalid
9 months ago
So seems like the group is on a roll this month! Hereâs our latest work on parametrising coarse-grained models of sugars (disaccharides) by Astrid Brandner & in collaboration with Iain Smith,
@pauloctsouza.bsky.social
and
@cg-martini.bsky.social
pubs.acs.org/doi/10.1021/...
#glycotime
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Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field
Sugars are ubiquitous in biology; they occur in all kingdoms of life. Despite their prevalence, they have often been somewhat neglected in studies of structureâdynamicsâfunction relationships of macro...
https://pubs.acs.org/doi/10.1021/acs.jcim.4c01874
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Elisa Frezza
9 months ago
The registration for the next GGMM2025 is now open. We are looking forward to meeting all of you in Forges-les-Eaux
#youngresearchers
#molecularmodelling
ggmm2025.sciencesconf.org
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XXIVÚmes journées du GGMM - Sciencesconf.org
https://ggmm2025.sciencesconf.org
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Alex MacKerell
9 months ago
Yes, Martin died peacefully at home in his sleep Saturday evening. His impact was large and on many levels for those of us that had the opportunity to work with him.
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Fabio Lolicato
9 months ago
Huge đšLipid Timeđš for
#compchem
Community! The release of the new set of
#Martini3
parametrizations for a wide range of lipid types is now out on
@chemrxiv.bsky.social
This milestone marks a huge step forward for simulations of lipid systems and their interactions.
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Dr. Hab Sophie Sacquin-Mora
10 months ago
@samuelmurail.bsky.social
is our last speaker this morning.
#BAF24
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Dr. Hab Sophie Sacquin-Mora
10 months ago
Another week, another workshop at the IBPC. This time we're looking beyond AlphaFold and
@ataly.bsky.social
gives the opening words
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Max Bonomi
10 months ago
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 đ
research.pasteur.fr/b/15Hr
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One PhD thesis in integrative structural biology | Research - Institut Pasteur
https://research.pasteur.fr/b/15Hr
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Dr Andrew Buchanan
10 months ago
Love this insight on the AI tools Alphafold 3, Boltz and Chai-1 in antibody engineering (my day job). âIt appears that these models well understand how antibodies fold, but not how they bind.â Thanks
@btnaughton.bsky.social
Post:
blog.booleanbiotech.com/alphafold3-b...
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Dr. Hab Sophie Sacquin-Mora
10 months ago
Le LBT se cherche un·e administrateurice systĂšmes et rĂ©seaux. Pour le moment le poste est ouvert en NOEMI (mobilitĂ©), donc si vous ĂȘtes dĂ©jĂ en poste et souhaitez nous rejoindre, c'est par ici !
mobiliteinterne.cnrs.fr/ords/afip/ow...
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Arne Elofsson
10 months ago
Stone conclusion by hearsay from day 1 at
#CASP16
all top methods used AF3 somehow. Improvements are made by increased sampling (FFT etc), ranking of models still a challenge. Some improvement on antibodies.
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Konstantin Korotkov
10 months ago
Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold.
#CASP16
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Jorge Bravo Abad
10 months ago
SurfDock: a surface-informed diffusion generative model for proteinâligand docking excels in accuracy, generalizability, and flexible ligand handling. It identified 7 novel ALDH1B1 inhibitors, showcasing its drug discovery potential.
nature.com/articles/s41...
Preprint:
biorxiv.org/content/10.1...
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SurfDock is a surface-informed diffusion generative model for reliable and accurate proteinâligand complex prediction - Nature Methods
SurfDock is a method for predicting proteinâligand complex structures by leveraging multimodal protein information and generative diffusion frameworks. Its results can be generalized to unseen protein...
https://nature.com/articles/s41592-024-02516-y
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Eric Lagadec
10 months ago
Attention, cascade réalisée sur X, n'essayez pas de la reproduire chez vous, c'est pour les professionnels. Des journalistes n'en ont plus rien à faire des faits, et l'on devrait débattre sur la rotondité de la Terre.... Attention, parole subversive "La Terre n'est pas plate!"
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10 months ago
Save the date! The 24th GGMM Congress will be held in Normandy from 10 to 12 June 2025. A great conference bringing together the best in molecular modelling.
#GGMM
ggmm2025.sciencesconf.org
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XXIVÚmes journées du GGMM - Sciencesconf.org
https://ggmm2025.sciencesconf.org/
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Gabriele Corso
10 months ago
Weâre excited to release a major update to the Boltz repo: v0.3.0. This release contains several important new features, including our confidence model and memory-efficient inference. Give it a try!
github.com/jwohlwend/bo...
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GitHub - jwohlwend/boltz: Official repository for the Boltz-1 biomolecular interaction model
Official repository for the Boltz-1 biomolecular interaction model - jwohlwend/boltz
https://github.com/jwohlwend/boltz
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Antoine Taly
10 months ago
Another paper showing that Alphafold remembers at least as much as it learned: Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much M Lazou, et al.
www.pnas.org/doi/abs/10.1...
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https://www.pnas.org/doi/abs/10.1073/pnas.2412719121
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Antoine Taly
10 months ago
Interested in a
#PhD
at the interface between structural biology and AI? ==> open call for a nice project proposed by Laura Baciou in collaboration with our lab. We will be happy to tell you more about it! Applications per se are through the U. Paris Saclay portal:
adum.fr/as/ed/voirpr...
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https://adum.fr/as/ed/voirproposition.pl?site=PSaclay&matricule_prop=59347&langue=en
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Dr. Hab Sophie Sacquin-Mora
10 months ago
We now have
@samuelmurail.bsky.social
on the stage, to talk about solute tempering.
#LBTdays2024
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Ălise DubouĂ©-Dijon
10 months ago
#LBTdays2024
fully updated program, with all titles. See you there tomorrow !
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Gabriele Corso
11 months ago
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
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