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Dheeraj Prakaash

@dheerajprakaash.bsky.social
593 followers 183 following 40 posts

Comp #Biophysics #Biochemistry Multiscale #simulations of #biomolecules #Postdoc (2025-P): Bidone group @sci.utah.edu @utah.edu #Postdoc (2022-24): Khalid group #Oxford Uni @ox.ac.uk #PhD (2019-22): Kalli group @universityofleeds.bsky.social

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Reposted by Dheeraj Prakaash
Leah @hoxinsocks.bsky.social · 29/09/2026
#TubulinTuesday!!
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Reposted by Dheeraj Prakaash
Leah @hoxinsocks.bsky.social · 21h
#TubulinTuesday!
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/07/2026
It's nice when you benchmark your own method and find it good. But its even nicer when others benchmark your method and find it good. Figure from: Coarse-grained simulations of long intrinsically disordered proteins: a benchmark of Martini 3 force-fields doi.org/10.64898/202...
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 16/07/2026
Casual reminder for #GROMACS users: Individual #trajectories are not reproducible, but the metrics derived from them can be (and usually are, under the same conditions and with sufficient sampling). Explained here: manual.gromacs.org/current/user... #simulations #compchem
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 05/12/2025
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...
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Syma Khalid @sykhalid.bsky.social · 05/12/2025
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.
nature.com
Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane - Communications Biology
Multi-scale molecular dynamics simulations reveal that polymyxins form polymyxin-protein aggregates upon associating with the E. coli outer membrane thereby reducing lateral mobility of outer membrane...
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 01/11/2025
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.
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 11/10/2025
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
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Rafael C. Bernardi @rcbernardi.bsky.social · 17/02/2025
🚀 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...
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David B. Sauer @davidbsauer.bsky.social · 16/01/2025
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...
nature.com
Transport and inhibition of the sphingosine-1-phosphate exporter SPNS2 - Nature Communications
SPNS2 exports S1P and FTY720-P to control immune cell migration. Here, the authors use cryo-EM, immunofluorescence, in vitro binding and in vivo S1P export, and MD simulations to uncover the mechanism...
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Reposted by Dheeraj Prakaash
Siewert-Jan Marrink @cg-martini.bsky.social · 27/12/2024
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...
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 18/12/2024
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.
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Ragothaman Yennamalli @structbioinfo.bsky.social · 18/12/2024
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.
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 16/12/2024
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...
rcsb.org
Watch the Webinar: Python Scripting for Molecular Docking
This virtual course introduces life scientists to the power and flexibility of Python Scripting for Molecular Docking
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João Rodrigues @jpglmrodrigues.bsky.social · 13/12/2024
I guess we have Boltz-1 to thank for pushing all these other AF3 clones to adopt fully open-source licenses and models.
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Alexey Amunts @amunts.bsky.social · 14/12/2024
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...
rbvi.ucsf.edu
Download UCSF ChimeraX
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Arvind Ramanathan @ramanathanlab.bsky.social · 26/11/2024
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
youtu.be
NVIDIA SC24 Special Address
YouTube video by NVIDIA
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AlphaFold Unofficial @alphafold.bsky.social · 10/12/2024
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...
nytimes.com
Google Makes New Quantum Computing Breakthrough
Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)
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Razvan Borza @rborza.bsky.social · 03/12/2024
📢 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...
On the left is the structural output from the AlphaFold 3 server colored by pLDDT, which requires structural knowledge for interpretation. On the right is the AlphaBridge ring output, where the results are pre-analyzed and visually presented, making them easier to understand.
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Razvan Borza @rborza.bsky.social · 05/11/2024
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...
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Harmit Singh Malik @harmitmalik.bsky.social · 09/12/2024
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/
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Harmit Singh Malik @harmitmalik.bsky.social · 09/12/2024
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
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AlphaFold Unofficial @alphafold.bsky.social · 07/12/2024
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...
deepmind.google
AlphaProteo generates novel proteins for biology and health research
New AI system designs proteins that successfully bind to target molecules, with potential for advancing drug design, disease understanding and more.
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Isabell Grothaus @isabellgrothaus.bsky.social · 06/12/2024
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
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 05/12/2024
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...
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Syma Khalid @sykhalid.bsky.social · 04/12/2024
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/....
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Michael Bauer @michaeldbauer.bsky.social · 26/11/2024
"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
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Itai Yanai @itaiyanai.bsky.social · 28/11/2024
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
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 26/11/2024
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?
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 27/11/2024
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
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Diego del Alamo @delalamo.xyz · 27/11/2024
Conformational dynamics smoothen the fitness landscapes of enzymes. Who knew? 🧪🧶
Another important biophysical factor underlying how fitness landscapes are traversed during evolution is conformational sampling, i.e. the ability of proteins to adopt multiple conformational substates.48,49 Different conformational substates could have different activities and thus contribute differently to the net fitness of the protein: conformation “A” could represent 5% of the populated states, but catalyze a new reaction that the other conformations cannot. Evolution can then act to smoothly “tune” the function of the protein through remote mutations that shift its conformational equilibrium by relatively stabilizing conformation “A”. This results in a smoother landscape because there are generally many more pathways by which a pre-existing conformational equilibrium between two conformations can be affected by remote mutations than the number of solutions that are available through complete remodeling of an active site. For example, the laboratory evolution of phosphotriesterase into an into arylesterase was tracked with protein crystallography, which revealed that almost all the mutations were remote from the active site and shifted the conformational equilibrium to favor pre-existing states that were beneficial to the new catalytic activity (50). The same process was observed in the evolution of a computationally designed Kemp eliminase, wherein gradual changes in the conformational sampling between inactive and active states resulting in a remarkably smooth evolutionary transition (51). These examples of evolutionary trajectories generated by laboratory evolution demonstrate how conformational flexibility can produce smooth fitness landscapes, and help explain the high frequency of remote mutations observed in evolutionary trajectories (52).
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Elisa Fadda @elisafadda.bsky.social · 13/11/2024
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
artistic rendition of glycoproteins 3D structures anchored on the cell surface and soluble with the glycans restored with https://glycoshape.org
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Itai Yanai @itaiyanai.bsky.social · 24/11/2024
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....
https://www.pnas.org/doi/epub/10.1073/pnas.2315735121
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Garrett @glarson96.bsky.social · 25/11/2024
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!
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AlphaFold Unofficial @alphafold.bsky.social · 24/11/2024
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
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Paulo C. T. Souza @pauloctsouza.bsky.social · 24/11/2024
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/...
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Diego del Alamo @delalamo.xyz · 24/11/2024
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
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 24/11/2024
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
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Stephen Turner @stephenturner.us · 14/11/2024
How to write an excellent Review article www.nature.com/articles/s44222-024-… (read free: rdcu.be/d0aKY)
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Itai Yanai @itaiyanai.bsky.social · 24/11/2024
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.
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Rafeeque Mavoor @rafeequemavoor.bsky.social · 20/11/2024
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
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 22/11/2024
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
SARS-Cov-2 virus particles.
Spike protein coordinates taken from RCSB PDB: 3JCL. Graphics made with Blender3D.Made with Blender3D.Protein coordinates taken from RCSB PDB: 8G92. Graphics made with Blender3D.
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Dheeraj Prakaash @dheerajprakaash.bsky.social · 22/11/2024
#trend continued :) Who's next? :P shiny.rcg.sfu.ca/u/rdmorin/sc...
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Marwin Segler @marwinsegler.bsky.social · 12/11/2024
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
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Andy Aydın-Aitchison @andy8chi.bsky.social · 21/11/2024
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 snip of my profile. Banner image incldes Arendt, Durkheim, Fanon and others drawn rouglys on eggs in Black and White. Profile picture is me in front of some autumn leaves. 
Key descriptive text identifies me as a criminologist working on atrocity crime. 
At the bottom, highlighted by a big red arrow is my ORCID ID: 0000-0002-7463-1302A snip from my ORCID profile page - at the left is a list of institutional and other links to social media, including one to Bluesky, highlighted by a big red arrow.
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Sergey Ovchinnikov @sokrypton.org · 22/11/2024
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...
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YC Lin @yiechanglin.bsky.social · 19/11/2024
I made a MD starter pack! Dm or reply to be added ☺️☺️ go.bsky.app/QQjPjbL
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David Vilchez @thevilchezlab.bsky.social · 18/11/2024
Bioart: a cool freeware alternative to Biorender bioart.niaid.nih.gov from the NIH
bioart.niaid.nih.gov
Bioart
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