Aninda Dutta
@anindadutta.bsky.social
PhD candidate (Biophysical chemistry) at the Columbus Lab, University of Virginia
Reposted by Aninda Dutta
They found Dr. Brenner’s notebook and of course it was always about Arginine #StrangerThings
December 27, 2025 at 9:25 PM
They found Dr. Brenner’s notebook and of course it was always about Arginine #StrangerThings
Reposted by Aninda Dutta
Check out our latest work on the discovery and engineering of PiggyBac transposases! 🧵
Discovery and protein language model-guided design of hyperactive transposases - @marcguellc.bsky.social @upf.edu @icreacommunity.bsky.social @crg.eu go.nature.com/4gXLGEw
Discovery and protein language model-guided design of hyperactive transposases - Nature Biotechnology
Phylogenetic mining and protein language models uncover improved PiggyBac transposase sequences.
go.nature.com
October 2, 2025 at 6:09 PM
Check out our latest work on the discovery and engineering of PiggyBac transposases! 🧵
Reposted by Aninda Dutta
Negative design enables cell-free expression and folding of designed transmembrane β-Barrels https://www.biorxiv.org/content/10.1101/2025.09.16.676539v1
September 18, 2025 at 11:49 PM
Negative design enables cell-free expression and folding of designed transmembrane β-Barrels https://www.biorxiv.org/content/10.1101/2025.09.16.676539v1
Reposted by Aninda Dutta
Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)
August 17, 2025 at 8:16 PM
Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)
Reposted by Aninda Dutta
Deep learning-based joint sequence-structure de novo membrane protein design https://www.biorxiv.org/content/10.1101/2025.08.15.670493v1
August 16, 2025 at 3:48 AM
Deep learning-based joint sequence-structure de novo membrane protein design https://www.biorxiv.org/content/10.1101/2025.08.15.670493v1
Reposted by Aninda Dutta
Evolutionarily diverse caveolins share a common structural framework built around amphipathic disks pubmed.ncbi.nlm.nih.gov/40772930/ #cryoem
August 8, 2025 at 8:19 PM
Evolutionarily diverse caveolins share a common structural framework built around amphipathic disks pubmed.ncbi.nlm.nih.gov/40772930/ #cryoem
Reposted by Aninda Dutta
Complexity myths and the misappropriation of evolutionary theory | PNAS 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
August 1, 2025 at 7:06 PM
Complexity myths and the misappropriation of evolutionary theory | PNAS www.pnas.org/doi/10.1073/...
Reposted by Aninda Dutta
We’re getting more and more papers on de novo protein design, but I still don’t really know what it means
What’s your definition of de novo design?
What’s your definition of de novo design?
January 4, 2025 at 10:50 PM
We’re getting more and more papers on de novo protein design, but I still don’t really know what it means
What’s your definition of de novo design?
What’s your definition of de novo design?
Reposted by Aninda Dutta
The brain activates front-line immune cells in response to the mere sight of a sick person
go.nature.com/475cIXn
go.nature.com/475cIXn
The brain fires up immune cells when sick people are nearby
When people viewed virtual avatars with coughs or rashes, their brains triggered an immune response.
go.nature.com
July 29, 2025 at 12:07 PM
The brain activates front-line immune cells in response to the mere sight of a sick person
go.nature.com/475cIXn
go.nature.com/475cIXn
Sucks at times.
1/ You’re merging gene data across tools. Suddenly nothing matches.
ENSEMBL, ENTREZ, TP53, P53…
Why so many gene IDs?
ENSEMBL, ENTREZ, TP53, P53…
Why so many gene IDs?
July 24, 2025 at 2:12 PM
Sucks at times.
Reposted by Aninda Dutta
Madhavi Krishnans lab with an absolutely amazing new measurement technique:
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip
Size and shape are critical discriminators between molecular species and states. We describe a microchip-based high-throughput imaging approach offering rapid and precise determination of molecular pr...
www.science.org
May 9, 2025 at 8:12 AM
Madhavi Krishnans lab with an absolutely amazing new measurement technique:
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Measurements of molecular size and shape on a chip | Science www.science.org/doi/10.1126/...
Reposted by Aninda Dutta
Why are biological membranes asymmetric, with different lipids in the two bilayer leaflets? Discovered in the 70s, lipid asymmetry is linked to many cellular processes, but why the cell needs it is largely unclear. @pavelbarahtjan.bsky.social addresses this question: www.biorxiv.org/content/10.1...
May 6, 2025 at 9:01 AM
Why are biological membranes asymmetric, with different lipids in the two bilayer leaflets? Discovered in the 70s, lipid asymmetry is linked to many cellular processes, but why the cell needs it is largely unclear. @pavelbarahtjan.bsky.social addresses this question: www.biorxiv.org/content/10.1...
Reposted by Aninda Dutta
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
Hey #TeamTomo,
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging?
That's why @florentwaltz.bsky.social and I made this website!
tomoguide.github.io
Follow the thread 1 /🧵
#CryoET #CryoEM 🔬🧪
Reposted by Aninda Dutta
Functional and Structural Characterization of F1-ATPase with common ancestral core domains in stator ring www.biorxiv.org/content/10.1101/2025.04.30.651372v1 #cryoem
May 3, 2025 at 1:27 PM
Functional and Structural Characterization of F1-ATPase with common ancestral core domains in stator ring www.biorxiv.org/content/10.1101/2025.04.30.651372v1 #cryoem
Reposted by Aninda Dutta
🚨New preprint!🚨 #teamtomo
We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles.
Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles.
Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
Surface morphometrics reveals local membrane thickness variation in organellar subcompartments https://www.biorxiv.org/content/10.1101/2025.04.30.651574v1
May 1, 2025 at 7:42 PM
🚨New preprint!🚨 #teamtomo
We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles.
Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles.
Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
Reposted by Aninda Dutta
If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”?
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
May 3, 2025 at 12:40 PM
If u ever had to depict proteins as schematics in papers, u know the dilemma: how to create a pretty “blob”?
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
If structure ends up big & central, u’ll render it with PyMol et al, but for a truly schematic depiction u want a biorender-style icon, but for YOUR protein.
Think I’ve finally found a way.
Reposted by Aninda Dutta
quite extraordinary story. Sometimes I think it’s the weird people that will save the world,
May 3, 2025 at 5:40 AM
quite extraordinary story. Sometimes I think it’s the weird people that will save the world,
Reposted by Aninda Dutta
Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE pubmed.ncbi.nlm.nih.gov/40301322/ #cryoem
April 30, 2025 at 8:35 PM
Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE pubmed.ncbi.nlm.nih.gov/40301322/ #cryoem
Reposted by Aninda Dutta
Grappling with poorly-resolved ligand binding sites in #cryoEM maps?
Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality and reveal clearer ligand density!
guide.cryosparc.com/processing-d...
Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality and reveal clearer ligand density!
guide.cryosparc.com/processing-d...
April 29, 2025 at 3:22 PM
Grappling with poorly-resolved ligand binding sites in #cryoEM maps?
Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality and reveal clearer ligand density!
guide.cryosparc.com/processing-d...
Check out our new case study on a peptide ligand-bound GPCR showing how practical tips and features in #CryoSPARC v4.7 improve locally refined map quality and reveal clearer ligand density!
guide.cryosparc.com/processing-d...
Reposted by Aninda Dutta
My guidelines for exploratory data analysis
April 14, 2025 at 8:11 PM
My guidelines for exploratory data analysis
Reposted by Aninda Dutta
Curious about using artificial intelligence to boost your research? Here are the programs you shouldn’t miss
https://go.nature.com/4ls2K7a
https://go.nature.com/4ls2K7a
AI for research: the ultimate guide to choosing the right tool
Nature - Curious about using artificial intelligence to boost your research? Here are the programs you shouldn’t miss.
go.nature.com
April 12, 2025 at 10:23 AM
Curious about using artificial intelligence to boost your research? Here are the programs you shouldn’t miss
https://go.nature.com/4ls2K7a
https://go.nature.com/4ls2K7a
Reposted by Aninda Dutta
Groundbreaking study in Cell from @leventallab.bsky.social: phospholipid asymmetry is a defining feature of the plasma membrane and cholesterol fills the holes — major implications for how this membrane works. A #lipidtime must-read! www.cell.com/cell/abstrac...
Cell membranes sustain phospholipid imbalance via cholesterol asymmetry
This work challenges a major assumption in cell biology by showing that lipid bilayers
can have drastically different phospholipid abundances between their two leaflets.
This lipid abundance asymmetry...
www.cell.com
April 3, 2025 at 3:07 PM
Groundbreaking study in Cell from @leventallab.bsky.social: phospholipid asymmetry is a defining feature of the plasma membrane and cholesterol fills the holes — major implications for how this membrane works. A #lipidtime must-read! www.cell.com/cell/abstrac...
Reposted by Aninda Dutta
The coming decade might see major cuts to US Government #funding for biomedicine. This Perspective highlights how your biosciences #PhD gives you the problem-solving skills to navigate this maelstrom, especially if you maintain flexibility, optimism &enthusiasm for uncharted paths🧪
▶️ plos.io/3XEKPjt
▶️ plos.io/3XEKPjt
Navigating your US bioscience career into the 2030s
The coming decade might see major cuts to US Government funding for biomedicine and the mainstreaming of pseudoscience. This Perspective highlights how your biosciences PhD gives you the problem-solvi...
plos.io
March 31, 2025 at 8:44 AM
The coming decade might see major cuts to US Government #funding for biomedicine. This Perspective highlights how your biosciences #PhD gives you the problem-solving skills to navigate this maelstrom, especially if you maintain flexibility, optimism &enthusiasm for uncharted paths🧪
▶️ plos.io/3XEKPjt
▶️ plos.io/3XEKPjt
Reposted by Aninda Dutta
Please watch. Powerful and chilling. 1: ‘Do not obey in advance.’ 20: ‘Be as courageous as you can!’
Here is my best guidance for action, rendered beautifully by the great John Lithgow. I first published these lessons more than eight years ago, in late 2016. They open the twenty chapters of "On Tyranny: Twenty Lessons from the Twentieth Century."
snyder.substack.com/p/twenty-les...
snyder.substack.com/p/twenty-les...
Twenty Lessons, read by John Lithgow
Key selections from On Tyranny, for viewing and sharing
snyder.substack.com
March 30, 2025 at 9:09 PM
Please watch. Powerful and chilling. 1: ‘Do not obey in advance.’ 20: ‘Be as courageous as you can!’
Reposted by Aninda Dutta
Molecule-MCP is a very cool tool connecting PyMOL and ChimeraX directly to Claude through the Model Context Protocol for prompt-assisted molecule modelling. Great stuff by Jinyuan Sun et al
github.com/ChatMol/mole...
github.com/ChatMol/mole...
March 22, 2025 at 5:55 PM
Molecule-MCP is a very cool tool connecting PyMOL and ChimeraX directly to Claude through the Model Context Protocol for prompt-assisted molecule modelling. Great stuff by Jinyuan Sun et al
github.com/ChatMol/mole...
github.com/ChatMol/mole...