Dr J
@gormanlab.bsky.social
Using structural biology to advance vaccine design.
(Views are my own)
(Views are my own)
Pinned
Dr J
@gormanlab.bsky.social
· Jan 17
Structural development of the HIV-1 apex-directed PGT145-PGDM1400 antibody lineage
The PGT145-PGDM1400 lineage targets the HIV-1 Env apex and belongs to the most potent
category of broadly neutralizing antibodies. Mason et al. describe the cryo-EM structures
of PGDM1400 and a PGT145...
www.cell.com
In our new Cell Reports paper we define the structure of the widely used quaternary specific bNAb PGDM1400 with HIV-1 Env. We also use our previous PGT145-SIV Env structure to improve PGT145 against other SIV strains and increase its HIV-1 breadth. www.cell.com/cell-reports...
Reposted by Dr J
Here is why friends don't let friends calculate FSC on denoised half-maps. I took EMD-17961, denoised the maps using Warp's Noise2Map, and calculated the FSC between various things. With noise gone from the half-maps, their consistency is no longer related to SSNR. Denoised map vs. model still works
December 15, 2025 at 1:53 AM
Here is why friends don't let friends calculate FSC on denoised half-maps. I took EMD-17961, denoised the maps using Warp's Noise2Map, and calculated the FSC between various things. With noise gone from the half-maps, their consistency is no longer related to SSNR. Denoised map vs. model still works
I've never used isonet but the images in this paper are amazing
Love the caption of Fig. 3 in this impressive preprint:
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
"A Goodsell-esque 3D orthogonal rendering of an IsoNet2-processed FIB-milled tomogram of C. reinhardtii"
doi.org/10.64898/202...
Since I am no expert, what does the cryoET community think of IsoNet? @cellarchlab.com
doi.org/10.1038/s414...
December 12, 2025 at 3:00 PM
I've never used isonet but the images in this paper are amazing
Reposted by Dr J
Reposted by Dr J
Researchers use AI and Reverse Vaccinology 2.0 on human blood samples to identify a potential new mpox target, and use the target in a vaccine that elicited mpox-neutralizing antibodies in mice. #ScienceTranslationalMedicine https://scim.ag/48Huqzj
Antigen-agnostic identification of poxvirus broadly neutralizing antibodies targeting OPG153
Antigen-agnostic isolation of B cells enabled the AI-assisted identification of broadly neutralizing antibodies targeting OPG153.
scim.ag
December 11, 2025 at 4:00 PM
Researchers use AI and Reverse Vaccinology 2.0 on human blood samples to identify a potential new mpox target, and use the target in a vaccine that elicited mpox-neutralizing antibodies in mice. #ScienceTranslationalMedicine https://scim.ag/48Huqzj
Reposted by Dr J
#onthisday Dec 9, 1979 the WHO certified that smallpox had been eradicated—the first human disease eliminated by coordinated global vaccination and surveillance, a landmark that transformed public health strategy worldwide #ScienceHistory
December 9, 2025 at 12:13 PM
#onthisday Dec 9, 1979 the WHO certified that smallpox had been eradicated—the first human disease eliminated by coordinated global vaccination and surveillance, a landmark that transformed public health strategy worldwide #ScienceHistory
A lot of the conversations yesterday were some version of -HepB used to be a problem so it made sense to vaccinate but now I don’t know anybody who’s gotten HepB so why are we still vaccinating?
And then the 2 reasonable people in the room flustered not knowing where to even begin.
And then the 2 reasonable people in the room flustered not knowing where to even begin.
December 6, 2025 at 5:01 PM
A lot of the conversations yesterday were some version of -HepB used to be a problem so it made sense to vaccinate but now I don’t know anybody who’s gotten HepB so why are we still vaccinating?
And then the 2 reasonable people in the room flustered not knowing where to even begin.
And then the 2 reasonable people in the room flustered not knowing where to even begin.
Paraphrasing:
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
December 6, 2025 at 4:57 PM
Paraphrasing:
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
-I think we should vote NO on the motion.
>We are not voting now, we are just discussing any proposed changes to the wording of the motion.
-I propose we remove all words from the motion.
Something that gets overlooked by a lot of bad takes on covid like the lab-leak theory or the current dismantling of the CDC is the we know at least 3 coronaviruses cross over in a 17 year period. There will likely be more and the next may be closer than we expect.
France is reporting two cases of MERS in two individuals who recently returned from the middle east. Both remain i hospital. MERS is caused by another coronavirus with spillover events occurring from usually from contact with camels.
www.cidrap.umn.edu/mers-cov/fra...
www.cidrap.umn.edu/mers-cov/fra...
France reports MERS in 2 travelers who had been to Middle East
No secondary transmission chains have been identified in France.
www.cidrap.umn.edu
December 5, 2025 at 7:27 PM
Something that gets overlooked by a lot of bad takes on covid like the lab-leak theory or the current dismantling of the CDC is the we know at least 3 coronaviruses cross over in a 17 year period. There will likely be more and the next may be closer than we expect.
Thread of vaccine studies with placebo controls
1/ Aaron Siri is presenting to ACIP right now. He's not a vaccine scientist. He's a plaintiff's attorney whose firm profits from vaccine-injury litigation, RFK Jr.'s personal lawyer, and someone who helped vet HHS leadership. He's now advising the committee that sets U.S. vaccine policy.
December 5, 2025 at 7:21 PM
Thread of vaccine studies with placebo controls
Reposted by Dr J
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5 - Nature Communications
This study reveals how the bat coronavirus HKU5 recognizes ACE2 receptors across mammals and birds, uncovering a cross-class receptor usage in coronaviruses and highlighting its potential for interspe...
www.nature.com
December 4, 2025 at 6:54 PM
Molecular insights into species-specific ACE2 recognition of coronavirus HKU5
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Pretty impressive to get 12 commissioners together...
12 former commissioners of the FDA came together to write a Perspectives piece for the New England Journal of Medicine; raising our concerns about recent changes to vaccine approval policy at the FDA and its implications for patients and public health.
December 4, 2025 at 5:12 PM
Pretty impressive to get 12 commissioners together...
Reposted by Dr J
If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs.
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
November 17, 2025 at 5:39 PM
If you'd like to celebrate the biology of viruses - or the fight against viral diseases - this winter, try out our free and updated #VirusSnowflake designs.
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Please share, and if you have any photos of Virus Snowflakes in your area it would be lovely to see them!
cvr-engagement.co.uk/virus-snowfl...
Reposted by Dr J
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
November 25, 2025 at 9:02 AM
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Reposted by Dr J
It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.
#virology #cryoEM
go.bsky.app/Qxv95BL
#virology #cryoEM
go.bsky.app/Qxv95BL
November 25, 2025 at 9:46 AM
It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know.
#virology #cryoEM
go.bsky.app/Qxv95BL
#virology #cryoEM
go.bsky.app/Qxv95BL
Reposted by Dr J
Exclusive: Scientists at the U.S. Centers for Disease Control and Prevention have been told to phase out all of their monkey research, Science has learned. https://scim.ag/48foQEk
Exclusive: CDC to end all monkey research
Studies related to HIV and other infectious diseases will be phased out, sources say; fate of the agency's animals remains unclear
www.science.org
November 21, 2025 at 3:08 PM
Exclusive: Scientists at the U.S. Centers for Disease Control and Prevention have been told to phase out all of their monkey research, Science has learned. https://scim.ag/48foQEk
Reposted by Dr J
Oh wow, this is 🤯 amazing: ~3-fold acceleration of running #relion on A100 GPUs for realistic single-particle refinement by the group of Guangwen Yang at @tsinghuauniversity.bsky.social
.
What a fantastic example of #OpenSoftwareAcceleratesScience, literally! 😍
dl.acm.org/doi/full/10....
.
What a fantastic example of #OpenSoftwareAcceleratesScience, literally! 😍
dl.acm.org/doi/full/10....
T2-RELION: Task Parallelism, Tensor Core Accelerated RELION for Cryo-EM 3D Reconstruction | Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
dl.acm.org
November 21, 2025 at 12:32 PM
Oh wow, this is 🤯 amazing: ~3-fold acceleration of running #relion on A100 GPUs for realistic single-particle refinement by the group of Guangwen Yang at @tsinghuauniversity.bsky.social
.
What a fantastic example of #OpenSoftwareAcceleratesScience, literally! 😍
dl.acm.org/doi/full/10....
.
What a fantastic example of #OpenSoftwareAcceleratesScience, literally! 😍
dl.acm.org/doi/full/10....
This is garbage. The scientific community wasted huge amounts of resources that should have gone into real vaccine safety or real autism research based on one garbage study that was not ignored, but found to be fraudulent, and then we kept researching a link at insane levels to be sure.
November 20, 2025 at 5:04 PM
This is garbage. The scientific community wasted huge amounts of resources that should have gone into real vaccine safety or real autism research based on one garbage study that was not ignored, but found to be fraudulent, and then we kept researching a link at insane levels to be sure.
Reposted by Dr J
at least @natsmb.nature.com is now asking the authors to make their structural data available to editors and reviewers prior to peer review
All journals should follow this example.
www.nature.com/articles/s41...
All journals should follow this example.
www.nature.com/articles/s41...
How we peer review structural data - Nature Structural & Molecular Biology
We explain why we ask our authors to provide structural data prior to peer review.
www.nature.com
November 13, 2025 at 12:57 PM
at least @natsmb.nature.com is now asking the authors to make their structural data available to editors and reviewers prior to peer review
All journals should follow this example.
www.nature.com/articles/s41...
All journals should follow this example.
www.nature.com/articles/s41...
AI is both super useful and super overblown in what it can do. It's like getting access to the internet. Some stuff is great and lots of things seem great but are really garbage. It's critical to be able to distinguish what to use it for and what to avoid using it for.
"existing AI tools are 'not great at actually finding the insightful pieces' within legislative and regulatory texts, according to Sanofi’s EU/AMEE head of regulatory science and policy, Rebecca Lumsden"
"while AI could 'give you a summary, you don’t get the insight.'"
"while AI could 'give you a summary, you don’t get the insight.'"
AI’s Attempt To Decode EU Pharma Reform Called A ‘Car Crash’
Sanofi’s EU regulatory science and policy head draws on a “nightmare” experience with using a generative AI tool to compare versions of the draft EU pharma reform text to explain the benefits and limi...
insights.citeline.com
November 13, 2025 at 4:29 PM
AI is both super useful and super overblown in what it can do. It's like getting access to the internet. Some stuff is great and lots of things seem great but are really garbage. It's critical to be able to distinguish what to use it for and what to avoid using it for.
Reposted by Dr J
Potent neutralization of Marburg virus by a vaccine-elicited antibody @nature.com @hhmi.org @veeslerlab.bsky.social @virbiotechnology.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 12, 2025 at 5:49 PM
Potent neutralization of Marburg virus by a vaccine-elicited antibody @nature.com @hhmi.org @veeslerlab.bsky.social @virbiotechnology.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Dr J
Our November issue is available at journals.iucr.org/d/issues/202...
On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg
On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg
November 5, 2025 at 1:29 PM
Our November issue is available at journals.iucr.org/d/issues/202...
On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg
On the cover: recent studies demonstrate that the range of samples suitable for cryo-EM single-particle analysis is expanding towards increasingly more native samples. Read the review at shorturl.at/mitjg
Reposted by Dr J
Now online! Generation of antigen-specific paired-chain antibodies using large language models
Generation of antigen-specific paired-chain antibodies using large language models
MAGE is a sequence-based protein language model designed to generate diverse human antibody sequences targeting various pathogens, including SARS-CoV-2, H5N1, and RSV-A. This AI-driven approach addresses traditional limitations by enabling efficient, target-agnostic antibody design with experimentally validated binding specificity.
dlvr.it
November 4, 2025 at 11:38 PM
Now online! Generation of antigen-specific paired-chain antibodies using large language models
Reposted by Dr J
🥳🥳🥳
Thrilled, and admittedly relieved, to see this major investment in Dutch #cryoEM become reality! 🇳🇱🔬
Honoured to be a co-applicant on this national initiative and very excited for the opportunity to advance our work in cellular structural virology! 🦠
www.uu.nl/en/news/33-m...
Honoured to be a co-applicant on this national initiative and very excited for the opportunity to advance our work in cellular structural virology! 🦠
www.uu.nl/en/news/33-m...
33 million euro investment for national electron microscope facility EMPower
A major new national facility for electron microscopy, called EMPower, has been awarded to a consortium of Dutch universities and medical centers. EMPower aims to pave the way for major discoveries im...
www.uu.nl
November 3, 2025 at 5:42 PM
🥳🥳🥳
Reposted by Dr J
Agency scientists speak out about the irreplaceable facilities, institutional knowledge and training opportunities that the USA is losing
go.nature.com/3WB8bFS
go.nature.com/3WB8bFS
Dismantling of US federal agencies will ‘destroy science’
From NASA to the National Institutes of Health, federal agencies conduct research that universities cannot. Agency scientists speak out about the irreplaceable facilities, institutional knowledge and training opportunities that the country is losing.
go.nature.com
November 3, 2025 at 12:24 PM
Agency scientists speak out about the irreplaceable facilities, institutional knowledge and training opportunities that the USA is losing
go.nature.com/3WB8bFS
go.nature.com/3WB8bFS