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

🚀 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...

submitted 86 days ago • 3 comments

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...

submitted 117 days ago • 0 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 138 days ago • 1 comment

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.

submitted 147 days ago • 1 comment

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.

submitted 147 days ago • 0 comments

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...

submitted 148 days ago • 0 comments

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

submitted 151 days ago • 1 comment

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...

submitted 151 days ago • 1 comment

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

submitted 169 days ago • 0 comments

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...

submitted 155 days ago • 0 comments

📢 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...

submitted 161 days ago • 3 comments

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...

submitted 190 days ago • 6 comments

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/

submitted 156 days ago • 80 comments

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...

submitted 157 days ago • 0 comments

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

submitted 159 days ago • 5 comments

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...

submitted 160 days ago • 0 comments

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/....

submitted 160 days ago • 3 comments

"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

submitted 169 days ago • 2 comments

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

submitted 166 days ago • 9 comments

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?

submitted 168 days ago • 11 comments

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

submitted 168 days ago • 1 comment

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

submitted 168 days ago • 2 comments

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

submitted 181 days ago • 5 comments

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....

submitted 170 days ago • 3 comments

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!

submitted 170 days ago • 4 comments

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

submitted 170 days ago • 0 comments

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/...

submitted 171 days ago • 1 comment

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

submitted 171 days ago • 7 comments

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

submitted 171 days ago • 1 comment

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

submitted 180 days ago • 2 comments

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.

submitted 171 days ago • 7 comments

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

submitted 174 days ago • 0 comments