We just dropped some science! 🔬📢 Thread 🧵: 1/4 - How do #antibiotic #polymyxins physically interact with the #E.coli outer #membrane (OM)? - How does this impact #large-scale #protein/LPS #diffusion in the OM? ..addressed in near-atomic detail @commsbio.nature.com: www.nature.com/articles/s42...

Our paper on polymyxin interacting with the E. coli outer membrane is out! Simulations by the very talented @dheerajprakaash.bsky.social www.nature.com/articles/s42... To scale outer membrane protein island simulated at coarse-grained resolution with portions refined at all atom resolution.

The #BidoneLab with costumes and scarfaces on for the #compchem #Halloween  potluck 🎃🍲 at the Henry Eyring Center (HEC) for Theoretical Chemistry. Thanks to our colleagues at the HEC @utahchemistry.bsky.social for organizing.

Happy to share that I have started as a #postdoc in the #BidoneLab at the Scientific Computing and Imaging Institute @uusci.bsky.social @utah.edu #SaltLakeCity, in collab with #VothGroup at UChicago @uchichemistry.bsky.social 👇🏻Pic of #beautiful #RockyMountains in #Utah from above the #clouds

🚀 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...

Our SPNS2 paper is published! A massive collaboration of Resolute, Oxford CMD, Nuvisan, @oxfordbiochemistry.bsky.social, CeMM, Bayer, & Univ. of Zurich Work of many talented colleagues, including @sykhalid.bsky.social @supertifurgalab.bsky.social and numerous others www.nature.com/articles/s41...

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...

Happy to inform that I've been accepted into the 11-month virtual postgrad program in #AI & #ML by @caltech.edu in collab with #IBM. Excited to dive into this field & upskill myself.

Academics and scientists should have a hobby. This is a necessity. Also, I think Bragg was able to do this since for half a day his admin and staff could handle or manage things without him.

Watch the Webinar: Python Scripting for Molecular Docki This virtual course introduces life scientists to the power and flexibility of python scripting www.rcsb.org/news/fe...

I guess we have Boltz-1 to thank for pushing all these other AF3 clones to adopt fully open-source licenses and models.

ChimeraX 1.9 has been released! Session view can now be automatically saved and restored. New ​'Find Cavities' tool identifying pockets in models. www.rbvi.ucsf.edu/chimerax/dow...

Really fortunate to have had the honor of being featured as part of NVIDIA SC24 special address by Jensen Huang and Ian Buck. This summarizes a lot of the work that is ongoing in the group highlighting the role of LLMs, multi modality and generative AI. youtu.be/eKzNKxWUeCE

Google’s quantum computer chip called Willow, needed less than five minutes to perform a mathematical calculation that one of the world’s most powerful supercomputers could not complete in 10 septillion years, a length of time exceeding the age of the known universe. www.nytimes.com/2024/12/09/t...

📢 Make your work FASTER and EASIER! Use AlphaBridge to analyze your AlphaFold results and receive a clear, easy-to-understand output—even for non-experts. ➡️ Let AlphaBridge help you accelerate your workflow! ❤️ Share and try it here: alpha-bridge.eu 👀Read more: www.biorxiv.org/content/10.1...

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔 ➡️ AlphaBridge will identify the most confident interactions, making your analysis easier! 🌐Try it here: alpha-bridge.eu 👀Read more: www.biorxiv.org/content/10.1...

I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/

But please dont share this as a mantra for success. If your success comes at the direct expense of your colleagues because they are doing all the work everyone is supposed to share in, it does not make you ‘successful’ it just makes you a horrible colleague. Also see peer review Rant over. For now

New AI system designs proteins that successfully bind to target molecules, with potential for advancing drug design, disease understanding and a system for designing novel, high-strength protein binders to serve as building blocks for biological and health research. deepmind.google/discover/blo...

Dear #comchem #glycotime folks 🍭, I need your help! Does anyone know a tool to build sulfated polysaccharides and get structure und topology files for GROMACS with CHARMM36 FF?🤔 Unfortunately Charmm-gui is placing sulfate groups in wrong orientations. Please RT! #moleculardynamics

Our paper: "OmpA controls order in the E. coli outer #membrane & shares the mechanical load" is out in @pnas.org - led by Georgina Benn and Thomas Silhavy. Collab b/w Princeton, NYU, UCL, & @oxfordbiochemistry.bsky.social. #Simulations by me & @sykhalid.bsky.social doi.org/10.1073/pnas...

In a multidisciplinary study led by Georgina Benn and Tom Silhavy we show the role of OmpA in controlling the organisation of the outer membrane and in sharing the mechanical load. www.pnas.org/doi/10.1073/....

"If we don't feel stupid it means we are not really trying" Very encouraging quote from this inspiring article. The other two are also excellent! I'll add this piece of advice, which a friendly ultramarathoner once gave me: "Enjoy the highs, manage the lows!" #econsky

If you submit your grants last minute, you're in good company. For the 2005 NIH Pioneer grant, half of the applications were submitted in the last two days. The red bars indicate the awardees. One awardee submitted 8 minutes before the deadline. bsky.app/profile/jere... @jeremymberg.bsky.social

What are some examples of weak-binding (approved) drugs? I think memantine binds NMDAR with an affinity of about 1µM. Are there other such examples?

Only a matter of time before #MassiveFold powers up⤴️ #protein #structure #prediction & #ProteinDesign #efficiency unlocking #AlphaFold 's true potential🧵 #academicsky #AI #research @alphafold.bsky.social #HPC #parallelization #compchem #compchemsky #Biology #Biochemistry #StructuralBiology #Science

Conformational dynamics smoothen the fitness landscapes of enzymes. Who knew? 🧪🧶

As we (my lab and I) are new here 😻, let me introduce some exciting #glycotime work we recently published in Nature Methods doi.org/10.1038/s415... GlycoShape is a completely OA database and toolbox to restore the 3D structure of glycans on glycoproteins 🥳 You can find it at glycoshape.org 1/2

How to write a grant? 1. The application is for the reviewer, not you, the applicant. 2. Communicate in stories. 3. Make your story cohesive—leave no puzzling gaps. 4. Make your story resonate to keep the reviewer reading. 5. Accept chance and noise in peer-review. www.pnas.org/doi/epub/10....

Anyone out there in #chemsky have any resources or personal experience about the transition from graduating with you PhD and then moving into industry. Specifically in the synthetic organic space, like how to look for the right job titles to apply for and what level of Scientist to look at. Thanks!

alphafoldserver.com/welcome AlphaFold Server can generate highly accurate biomolecular structure predictions containing proteins, DNA, RNA, ligands, ions, and model chemical modifications for proteins and nucleic acids. AI cannot replace the mind of a scientist but it certainly can compliment. #ai

Excited to share that our recent research using #Martini3 #CG simulations on the role of Spc2 in the yeast signal peptidase complex (SPC) has been published in the Journal of Cell Biology. Read the full article here: rupress.org/jcb/article/...

Anyone have a walkthrough for setting up MD simulations on the cloud (not Google Colab or equivalent)? Personal pet project so can’t use my employer’s resources

A #photograph of a #spider and its #vibrant super-silky web that I clicked with my flashlight on. Can't get enough of #Nature 's #beauty 🌈 #photography #samsung #smartphone #glowing #rainbow #spiderweb #wildlife #art #halloween #night #wild

How to write an excellent Review article https://www.nature.com/articles/s44222-024-00256-4 (read free: https://rdcu.be/d0aKY)

70% of scientists say they experience the imposter syndrome. I still experience it too sometimes, and what helps is talking with a science buddy with whom it’s ok to say stupid things, which may actually turn out to be good ideas.

Free alternaive for Chemdraw! 😍 A nice tool to draw chemical structures. This one has all the necessary features. Try 𝗞𝗲𝘁𝗰𝗵𝗲𝗿. (Open source) Share the post and spread the message. Ketcher link: lnkd.in/g2Xjnii4

Seems like I haven't yet mentioned that- I enjoy #SciArt #SciComm #SciViz #illustration. (Thread🧵) Inspired by and thanks to @rafeequemavoor.bsky.social @bradyajohnston.bsky.social @verenaresch.bsky.social @sarahjpiper.bsky.social for #Blender3d lessons. #CompBio #CompChem #CompChemSky

#trend continued :) Who's next? :P shiny.rcg.sfu.ca/u/rdmorin/sc...

go.bsky.app/Qc4frbt Made a starter pack for computational chemists, let me know who I missed please @jchodera.bsky.social @olexandr.bsky.social @jelfschem.bsky.social

Academics wanting to 'verify' their Bluesky profile as genuine might give an ORCID identifier in their profile and link back to their Bluesky profile from ORCID. #AcademicSky

A few more letters... and we can finally write amino acid sequence with protein structure encoded by amino acid sequence? 🧬🤔😀 @chrisfrank662.bsky.social , Dominik Schiwietz, Lara Fuss, Hendrik Dietz www.biorxiv.org/content/10.1...

I made a MD starter pack! Dm or reply to be added ☺️☺️ go.bsky.app/QQjPjbL

Bioart: a cool freeware alternative to Biorender bioart.niaid.nih.gov from the NIH

Hi all! Excited to explore, share & connect under the #BlueSky I completed my 1st postdoc w/ @sykhalid.bsky.social @ Oxford. Currently on the US job market to do another #postdoc. Interests: #compchem, #proteins, #membranes, multi-scale MD #simulations I'm into sports, hikes, dogs, motorbikes👇🏻 :)