Dheeraj Prakaash
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dheerajprakaash.bsky.social
Dheeraj Prakaash
@dheerajprakaash.bsky.social
570 followers 180 following 34 posts
Comp #Biophysics #Biochemistry
Multiscale MD #simulations of #biomolecules

Postdoc w/ Dr Tamara Bidone
SCI Institute @utah.edu

Previously:
Postdoc (2022-24) - Khalid group
Uni of Oxford @ox.ac.uk

PhD (2022) - Kalli group
@universityofleeds.bsky.social
Posts Replies Media Videos
dheerajprakaash.bsky.social
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.
November 1, 2025 at 4:51 AM
dheerajprakaash.bsky.social
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
October 11, 2025 at 8:34 PM
Reposted by Dheeraj Prakaash
rcbernardi.bsky.social
🚀 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...
February 17, 2025 at 6:56 AM
Reposted by Dheeraj Prakaash
davidbsauer.bsky.social
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...
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...
www.nature.com
January 16, 2025 at 6:17 PM
Reposted by Dheeraj Prakaash
cg-martini.bsky.social
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...
December 27, 2024 at 10:16 AM
dheerajprakaash.bsky.social
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.
December 18, 2024 at 7:25 AM
Reposted by Dheeraj Prakaash
structbioinfo.bsky.social
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.
lindorfflarsen.bsky.social Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Dec 17
This thread about academics and hobbies somehow reminded me of this story of Lawrence Bragg working part time and anonymously as a gardner because he missed having his own garden [from What Mad Pursuit]
December 18, 2024 at 4:08 AM
Reposted by Dheeraj Prakaash
rcsbpdb.bsky.social
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...
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
www.rcsb.org
December 16, 2024 at 5:12 PM
Reposted by Dheeraj Prakaash
jpglmrodrigues.bsky.social
I guess we have Boltz-1 to thank for pushing all these other AF3 clones to adopt fully open-source licenses and models.
December 13, 2024 at 4:55 PM
Reposted by Dheeraj Prakaash
amunts.bsky.social
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...
Download UCSF ChimeraX
www.rbvi.ucsf.edu
December 14, 2024 at 9:08 AM
Reposted by Dheeraj Prakaash
ramanathanlab.bsky.social
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
NVIDIA SC24 Special Address
YouTube video by NVIDIA
youtu.be
November 26, 2024 at 5:00 AM
Reposted by Dheeraj Prakaash
alphafold.bsky.social
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...
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.)
www.nytimes.com
December 10, 2024 at 1:16 AM
Reposted by Dheeraj Prakaash
rborza.bsky.social
📢 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.
December 3, 2024 at 11:15 PM
Reposted by Dheeraj Prakaash
rborza.bsky.social
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...
November 5, 2024 at 12:18 AM
Reposted by Dheeraj Prakaash
harmitmalik.bsky.social
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/
December 9, 2024 at 3:16 AM
Reposted by Dheeraj Prakaash
harmitmalik.bsky.social
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
December 9, 2024 at 3:26 AM
Reposted by Dheeraj Prakaash
alphafold.bsky.social
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...
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.
deepmind.google
December 7, 2024 at 1:42 PM
Reposted by Dheeraj Prakaash
isabellgrothaus.bsky.social
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
December 6, 2024 at 7:48 AM
dheerajprakaash.bsky.social
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...
December 5, 2024 at 8:30 AM
Reposted by Dheeraj Prakaash
sykhalid.bsky.social
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
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...
www.pnas.org
December 4, 2024 at 10:07 PM
Reposted by Dheeraj Prakaash
michaeldbauer.bsky.social
"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
scinews.bsky.social Science News @scinews.bsky.social · Nov 24
Three must read papers for PhD students. #scisky #PhD #science #research #academicsky

1. The importance of stupidity in scientific research

Open Access
journals.biologists.com/jcs/article/...
November 26, 2024 at 2:04 AM
Reposted by Dheeraj Prakaash
itaiyanai.bsky.social
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
November 28, 2024 at 2:18 PM
Reposted by Dheeraj Prakaash
lindorfflarsen.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?
November 26, 2024 at 9:25 PM
dheerajprakaash.bsky.social
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
November 27, 2024 at 8:14 AM
Reposted by Dheeraj Prakaash
delalamo.xyz
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).
November 27, 2024 at 4:17 AM