cen0ten.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Register Now for the Webinar on "Streamlining Access to RCSB PDB APIs with Python" on Monday March 24 pdb101.rcsb.org/news...

submitted 8 days ago • 0 comments

Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN https://www.biorxiv.org/content/10.1101/2025.02.13.637498v1

submitted 9 days ago • 0 comments

First direct chemical synthesis of a gene over 1700 nucleotides long covered by @chemistryworld.com! Read the full paper in Chemical Science (which is free to read!) here: pubs.rsc.org/en/content/a... #ChemSky 🧪 #ChemBio

submitted 15 days ago • 2 comments

RT please: Just 1.5 months away from our joint 3DBioinfo/3DSIG amazing conference! These are our two great keynote speakers! @rolanddunbrack.bsky.social & @silviaosuna.bsky.social! Check our preliminary programme here: www.iscb.org/3dbioinfo202... Registration link: www.iscb.org/3dbioinfo202...

submitted 13 days ago • 1 comment

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)

submitted 18 days ago • 4 comments

"Frustration In Physiology And Molecular Medicine" arxiv.org/abs/2502.03851 Our latest review is online! The table of contents is crazy!! Everything you wanted to know!! We review the physics concepts, applications in proteins, diseases & even how frustration could be useful to study the brain!

submitted 19 days ago • 0 comments

PSA: Digging into Chai-1 and found out that it gives different protein-ligand structures & confidences depending on the SMILES canonicalization used May also be the case with AF3 & Boltz-1, but haven't verified As to what this means... see the rest of the thread 🧵

submitted 22 days ago • 1 comment

Molecular mechanisms of inverse agonism via κ-opioid receptor–G protein complexes. @nchembio Check the #cryoEM #structure of this #membrane #protein in the UniTmp database: https://pdbtm.unitmp.org/entry/8vvf

submitted 23 days ago • 0 comments

Evidencing three factors for postdoc contribution to future career success (mobility, fellowship, hit paper), a good study to discuss in lab meetings. doi.org/10.1073/pnas...

submitted 25 days ago • 0 comments

If I had a coin for every time I have read this paper... The reasoning they used to derive the occurrence of superfolds by starting with the hypothesis of having equally populated folds given the data available 30 years ago... beautiful!!! It is just poetry! nature.com/articles/372...

submitted 26 days ago • 0 comments

IonBench: a benchmark of optimisation strategies for mathematical models of ion channel currents https://www.biorxiv.org/content/10.1101/2025.01.31.635876v1

submitted 26 days ago • 0 comments

It’s incredibly hard to study lipids in biological membranes on the nanoscale. You need near-perfect information on both membrane ultrastructure and lipid density, which usually isn’t attainable. Lipid-CLEM brought to you by @mathilda95.bsky.social changes that. www.biorxiv.org/content/10.1...

submitted 26 days ago • 12 comments

Proud of my team @Sanofi in helping to write this monumental review for the use of computational tools (both from an MD perspective and AI/ML) in modeling LNPs. We hope it will illustrate the power of computation as a complementary approach to devise enhanced delivery solutions for therapeutics.

submitted 27 days ago • 0 comments

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

submitted 29 days ago • 0 comments

Atomic scale description of the allosteric coupling between a lipid bilayer and a membrane protein https://www.biorxiv.org/content/10.1101/2025.01.24.634742v1

submitted 30 days ago • 0 comments

Engineering a membrane protein chaperone to ameliorate the proteotoxicity of mutant huntingtin www.nature.com/articles/s41...

submitted 30 days ago • 0 comments

Benchmarking the effectiveness of feature extraction, finetuning, low-rank adaptation, and bottleneck adaptors for transfer learning with protein language models. Thomas Bikias, Evangelos Stamkopoulos, Sai. T. Reddy www.biorxiv.org/content/10.1...

submitted 33 days ago • 1 comment

I'd like to draw your attention to this truly excellent paper from the Taraska lab on cryoET of plasma membrane associated proteins. Everyone who is thinking about probes in the cryoET space should also see what they could do with ferritag (fig 6) www.nature.com/articles/s41...

submitted 35 days ago • 11 comments

You're invited to the HITS-SIMPLAIX Joint Colloquium titled "How can Generative AI help understand the Physics of Molecules?" on 27 January at 2:00 PM CET, featuring Simon Olsson @smnlssn.bsky.social. Participate on-site by emailing [email protected] or register via ow.ly/qBGP50UIfxt for Zoom access.

submitted 37 days ago • 0 comments

New preprint from our group! We propose SHAPES, a set of metrics to quantify the distributional coverage of generative models of protein structures with embeddings at different structural hierarchies and quantify undersampling / extrapolation behaviors.

submitted 42 days ago • 1 comment

(I’m only sharing this paper so I remember to read it when I get back from vacation) www.nature.com/articles/s41...

submitted 46 days ago • 1 comment

Groundbreaking work by @matthewkhoward.bsky.social and Nicholas Hoppe (not on bsky?) from the @willowcoyote.bsky.social @amanglik.bsky.social labs. Mapping function to structure with deep mutational scanning to resolve the mechanisms of pH sensing GPCRs www.sciencedirect.com/science/arti...

submitted 55 days ago • 3 comments

Why your transformer-based net does not generalized from small molecules to peptides? Well, here one of the reasons: arxiv.org/abs/2410.01104 Once you know the root of the problem, you can find nice solutions 😉 In our case, a very simple regularization term did the job.

submitted 59 days ago • 1 comment

Favourite paper of 2007 "Generalized neural-network representation of high-dimensional potential-energy surfaces" by Behler and Parrinello. (1/4) journals.aps.org/prl/abstract...

submitted 59 days ago • 1 comment

Hey #teamtomo checkout our #teamscience approach to #cellbio #cryoET I can’t thank @cellarchlab.com enough for this one 😍😍 Awesome team science from @mpibiochem.bsky.social @biozentrum.bsky.social Thermo Fisher Scientific and more #firstpost on Bluesky www.biorxiv.org/content/10.1...

submitted 59 days ago • 2 comments

Happy ending (of the year): the release of our preprint, "The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior", now available on @ChemRxiv. 👉 Read the full preprint here: chemrxiv.org/engage/chemr... and get the parameters here: github.com/Martini-Forc...

submitted 61 days ago • 1 comment

Mitochondria consist of networks of cylindrical tubes, right? Not necessarily! - in our new preprint, @gavsturm.bsky.social investigates how mitochondria transiently adopt a beads-on-a-string morphology www.biorxiv.org/content/10.1...

submitted 65 days ago • 6 comments

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

submitted 65 days ago • 2 comments

🧬 "MSA clustering enhances AF-Multimer's ability to predict conformational landscapes of protein-protein interactions" explores how MSA sampling improves #AlphaFold's performance in predicting binding mechanisms for proteins with multiple states. Learn more: doi.org/10.1093/bioa... #ProteinFolding

submitted 65 days ago • 1 comment

We’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...

submitted 108 days ago • 6 comments

Smart idea by Gnatzy et al. to screen for weakly binding #GPCR ligands: Fuse the extracellular domain of a class B GPCR to the transmembrane domain of target class A receptors. Link the screened compounds to a peptide that is known to bind this extracellular domain. pubs.acs.org/doi/abs/10.1...

submitted 66 days ago • 0 comments

Thomas Silhavy's Lab at Princeton investigated the role of the outer membrane protein OmpA in organizing the outer membrane protein lattice and mechanically coupling it to the cell wall, which enhances the overall strength and integrity of the cell envelope. www.pnas.org/doi/full/10....

submitted 67 days ago • 0 comments

Yes! Image is the second page from our writing guidelines, but of course reading is essential beyond just for writing. In addition to the points in the thread below, I also recommend practicing multiple tiers of reading (skim, browse figures, read, read in depth) github.com/KULL-Centre/...

submitted 68 days ago • 2 comments

Extremely honoured and excited to continue working on protein chirality and origin of life w. many dedicated group members & Johan Olsen. Thanks to @carlsbergfondet.dk for trusting us on this endeavour and to present and former group members for getting us here www.carlsbergfondet.dk/det-har-vi-s...

submitted 71 days ago • 2 comments

Coiled coils (CCs) are protein domains in which alpha helices assemble into regular supercoiled bundles. In our new paper, we investigate how accurately AlphaFold2 predicts the oligomeric state, topology, and fine structural details of CC domains: onlinelibrary.wiley.com/doi/10.1002/....

submitted 71 days ago • 0 comments

📣 Save the dates 📅 We are organizing a Benzon Symposium on "Protein structure prediction and design" with what I think is an amazing set of speakers Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and abstract submission will open in March (benzon-foundation.dk/benzon-sympo...)

submitted 75 days ago • 1 comment

How can randomness be a source of living order? Can physics explain how an embryo emerges out of chaos? In this new paper in Science, Bernat Corominas-Murtra, @ehannezo.bsky.social & cols. show how embryos solve their own Rubik’s cube ist.ac.at/en/news/from...

submitted 75 days ago • 2 comments

Incredibly happy to finally see our manuscript "Emergence of power-law distributions in protein-protein interaction networks through study bias" published in @elife.bsky.social. doi.org/10.7554/eLif... It's been a long but fun journey with @dbblumenthal.bsky.social and @martinschaefer.bsky.social

submitted 74 days ago • 1 comment

Predicting absolute protein folding stability using generative models @mcagiada.bsky.social @sokrypton.org & I used ESM-IF to predict ∆G for folding & conformational change Paper, code and colab 📜 dx.doi.org/10.1002/pro.... 💾 github.com/KULL-Centre/... 👩‍💻 colab.research.google.com/github/KULL-...

submitted 74 days ago • 1 comment

Sharing here a new commentary in Science Policy Forum that provides new analysis on risks related to the potential future creation of mirror bacteria — synthetic organisms in which all molecules have reversed chirality (i.e. are ‘mirrored’). 1/x www.science.org/doi/10.1126/...

submitted 76 days ago • 3 comments

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

submitted 77 days ago • 24 comments