Pranav NM Shah
@proteincapsid.bsky.social
Postdoc at STRUBI. Using cryo-EM to see viruses better.
"The result is a treadmill of constant activity with
limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized."
arxiv.org/pdf/2511.04820
Will the real scientists please stand up?
limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized."
arxiv.org/pdf/2511.04820
Will the real scientists please stand up?
arxiv.org
November 12, 2025 at 12:34 PM
"The result is a treadmill of constant activity with
limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized."
arxiv.org/pdf/2511.04820
Will the real scientists please stand up?
limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized."
arxiv.org/pdf/2511.04820
Will the real scientists please stand up?
Reposted by Pranav NM Shah
I'm pleased to announce 🍦 Icecream 🍨 v0.3!
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
November 5, 2025 at 2:41 PM
I'm pleased to announce 🍦 Icecream 🍨 v0.3!
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
Reposted by Pranav NM Shah
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
November 3, 2025 at 12:26 PM
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Reposted by Pranav NM Shah
Jeremy is an excellent scientist and leader. Highly recommended!
warwick.ac.uk/fac/cross_fa...
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
Dr Jeremy Keown
Dr Jeremy Keown
warwick.ac.uk
October 29, 2025 at 8:31 PM
Jeremy is an excellent scientist and leader. Highly recommended!
Reposted by Pranav NM Shah
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 29, 2025 at 9:17 AM
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Reposted by Pranav NM Shah
warwick.ac.uk/fac/cross_fa...
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
Dr Jeremy Keown
Dr Jeremy Keown
warwick.ac.uk
October 24, 2025 at 7:58 AM
warwick.ac.uk/fac/cross_fa...
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
I am advertising for a PhD position in my group. We'll be investigating how pathogenic RNA viruses replicate in the nucleus. The project will teach cryoEM/ET, virus culture, and in vitro assays.
If you're interested reach out and I'd be happy to have a chat.
Reposted by Pranav NM Shah
www.biorxiv.org/content/10.1...
Really excited to have our work out in the world. CCHFV has a 450kDa L-Protein, about twice the size of L-Proteins from other segmented RNA viruses. We have used cryoEM and functional assays to begin to understand it this massive multifunctional protein works.
Really excited to have our work out in the world. CCHFV has a 450kDa L-Protein, about twice the size of L-Proteins from other segmented RNA viruses. We have used cryoEM and functional assays to begin to understand it this massive multifunctional protein works.
Structural and functional characterisation of the Crimean-Congo Haemorrhagic Fever Virus RNA Dependent RNA Polymerase
Crimean-Congo Haemorrhagic Fever Virus (CCHFV) is found across Africa, Asia, and the Middle East where it can cause Haemorrhagic outbreaks with high case fatality rates. Central to the viral life cycl...
www.biorxiv.org
October 22, 2025 at 12:22 PM
www.biorxiv.org/content/10.1...
Really excited to have our work out in the world. CCHFV has a 450kDa L-Protein, about twice the size of L-Proteins from other segmented RNA viruses. We have used cryoEM and functional assays to begin to understand it this massive multifunctional protein works.
Really excited to have our work out in the world. CCHFV has a 450kDa L-Protein, about twice the size of L-Proteins from other segmented RNA viruses. We have used cryoEM and functional assays to begin to understand it this massive multifunctional protein works.
Reposted by Pranav NM Shah
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
Neat!
Ever wondered how to position organelles in bacteria? Wonder no more!
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
September 23, 2025 at 4:06 PM
Neat!
Nice one Flo @schurlab.bsky.social !
Cryo-ET visualization of HTT bound to F-actin, highlighted in the yellow square on the left.
On the right, a detailed zoom-in view of the molecular model of the HTT/F-actin complex is shown.
On the right, a detailed zoom-in view of the molecular model of the HTT/F-actin complex is shown.
September 22, 2025 at 5:09 PM
Nice one Flo @schurlab.bsky.social !
Reposted by Pranav NM Shah
Our aim was to create a kit to produce in-house 1.2 holey carbon cryoEM grids, in three simple steps, at less than half of the prize, and without due times. I think we are there. Academic teams that want to know more, receive training or order a kit, please contact grids@puxano.com.
August 18, 2025 at 7:02 PM
Our aim was to create a kit to produce in-house 1.2 holey carbon cryoEM grids, in three simple steps, at less than half of the prize, and without due times. I think we are there. Academic teams that want to know more, receive training or order a kit, please contact grids@puxano.com.
Reposted by Pranav NM Shah
Confidence-guided cryo-EM map optimisation with LocScale-2.0 www.biorxiv.org/content/10.1101/2025.09.11.674726v1 #cryoem
September 15, 2025 at 7:11 AM
Confidence-guided cryo-EM map optimisation with LocScale-2.0 www.biorxiv.org/content/10.1101/2025.09.11.674726v1 #cryoem
Reposted by Pranav NM Shah
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
September 15, 2025 at 7:39 AM
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
Reposted by Pranav NM Shah
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
September 13, 2025 at 12:05 AM
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
Reposted by Pranav NM Shah
Ben Vollmer and Kay Grunewald & team @cssbhamburg.bsky.social and the beautiful structure along important insights for herpesvirus entry and membrane fusion.
Prefusion gB of HSV bound with a neutralizing nanobody www.nature.com/articles/s41...
A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2 - Nature
A neutralizing nanobody specific to the prefusion conformation of herpes simplex virus glycoprotein B has cross-species activity and offers insights into virus neutralization, possible immunogens and ...
www.nature.com
September 4, 2025 at 7:36 AM
Ben Vollmer and Kay Grunewald & team @cssbhamburg.bsky.social and the beautiful structure along important insights for herpesvirus entry and membrane fusion.
Reposted by Pranav NM Shah
Researchers from CSSB & @mpi-nat.bsky.social have generated a highly potent nanobody that neutralizes a protein essential for the herpes virus infection. Published in @nature.com, the findings promise new therapies to treat & prevent infections @leibnizliv.bsky.social @uni-hamburg.de
t1p.de/cxt7a
t1p.de/cxt7a
September 4, 2025 at 8:03 AM
Researchers from CSSB & @mpi-nat.bsky.social have generated a highly potent nanobody that neutralizes a protein essential for the herpes virus infection. Published in @nature.com, the findings promise new therapies to treat & prevent infections @leibnizliv.bsky.social @uni-hamburg.de
t1p.de/cxt7a
t1p.de/cxt7a
Reposted by Pranav NM Shah
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Pranav NM Shah
One week left to apply for a fully funded PhD position in my group! Please repost. jobrxiv.org/job/max-plan...
PhD student in cryo-ET of membrane trafficking at MPI-NAT in Göttingen, DE
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
August 21, 2025 at 9:02 AM
One week left to apply for a fully funded PhD position in my group! Please repost. jobrxiv.org/job/max-plan...
Reposted by Pranav NM Shah
Very pleased to have our new work out where we perform a structure/function study on the bornavirus polymerase complex with fantastic coauthors. Have a read www.nature.com/articles/s41... @warwicklifesci.bsky.social @loiccarrique.bsky.social @franziskaguenl.bsky.social
The structure of the mammalian bornavirus polymerase complex - Nature Communications
Borna disease virus 1 replicates and transcribes its negative sense RNA genome in the nucleus of infected cells. Here, the authors present the cryoEM structures of the large polymerase protein in comp...
www.nature.com
August 13, 2025 at 12:13 PM
Very pleased to have our new work out where we perform a structure/function study on the bornavirus polymerase complex with fantastic coauthors. Have a read www.nature.com/articles/s41... @warwicklifesci.bsky.social @loiccarrique.bsky.social @franziskaguenl.bsky.social
Reposted by Pranav NM Shah
New Title Alert: Tomcat- a web-based tool designed for cataloging and managing tomography data providing an easy way to view, annotate, and organize tomograms.
Learn more here: buff.ly/75XbvPv
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/75XbvPv
#SBGrid #SBGridSoftware #StructuralBiology
GitHub - shahpnmlab/tomcat: Tomography Catalogue Tool
Tomography Catalogue Tool. Contribute to shahpnmlab/tomcat development by creating an account on GitHub.
buff.ly
July 21, 2025 at 4:11 PM
New Title Alert: Tomcat- a web-based tool designed for cataloging and managing tomography data providing an easy way to view, annotate, and organize tomograms.
Learn more here: buff.ly/75XbvPv
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/75XbvPv
#SBGrid #SBGridSoftware #StructuralBiology
Reposted by Pranav NM Shah
Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO www.biorxiv.org/content/10.1101/2025.07.17.665296v1 #cryoem
July 19, 2025 at 10:03 AM
Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO www.biorxiv.org/content/10.1101/2025.07.17.665296v1 #cryoem
Reposted by Pranav NM Shah
Latest preprint from the lab, many years in the making!
By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.
This could have big implications for our understanding of viral replication & assembly (🧵)
www.biorxiv.org/content/10.1...
By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.
This could have big implications for our understanding of viral replication & assembly (🧵)
www.biorxiv.org/content/10.1...
June 18, 2025 at 6:32 AM
Latest preprint from the lab, many years in the making!
By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.
This could have big implications for our understanding of viral replication & assembly (🧵)
www.biorxiv.org/content/10.1...
By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.
This could have big implications for our understanding of viral replication & assembly (🧵)
www.biorxiv.org/content/10.1...
Reposted by Pranav NM Shah
Proud to share our latest paper. doi.org/10.1016/j.cr...
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
June 17, 2025 at 10:59 AM
Proud to share our latest paper. doi.org/10.1016/j.cr...
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Through the dedication of @glynnca.bsky.social and @cryingem.bsky.social we report a thorough method to image molecular organisation within hippocampus tissue.
Structural biology in tissue is well and truly here!
@rosfrankinst.bsky.social
Reposted by Pranav NM Shah
Chromatic aberration (Cc) corrected cryo-EM: The structure of pseudorabies virus (PRV) using both zero-loss and energy loss electrons pubmed.ncbi.nlm.nih.gov/40499325/ #cryoem
June 12, 2025 at 3:48 PM
Chromatic aberration (Cc) corrected cryo-EM: The structure of pseudorabies virus (PRV) using both zero-loss and energy loss electrons pubmed.ncbi.nlm.nih.gov/40499325/ #cryoem
Reposted by Pranav NM Shah
June 6, 2025 at 3:14 PM