Ernst Schmid
@ernstschmid.bsky.social
Full stack developer who occasionally wears a lab coat. Currently a machine learning researcher at Manifold Bio.
Reposted by Ernst Schmid
Fer’s tour de force in B. anthracis is out! Fer got Tn-seq running, built an ordered knockout library, defined all essential sporulation genes, and found a peptidoglycan deacetylase inhibitor critical for engulfment. Including our first one-by-all Alphafold screen! journals.plos.org/plosbiology/...
Identification of sporulation genes in Bacillus anthracis highlights similarities and significant differences with Bacillus subtilis
How good is Bacillus subtilis as a model for the spore-forming pathogen Bacillus anthracis? Using high throughput genetics to identify B. anthracis sporulation genes and cytological analysis of the mu...
journals.plos.org
December 13, 2025 at 4:53 PM
Fer’s tour de force in B. anthracis is out! Fer got Tn-seq running, built an ordered knockout library, defined all essential sporulation genes, and found a peptidoglycan deacetylase inhibitor critical for engulfment. Including our first one-by-all Alphafold screen! journals.plos.org/plosbiology/...
Reposted by Ernst Schmid
How to keep in step when your (protein) partner speeds up…
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
www.science.org
November 28, 2025 at 5:22 PM
How to keep in step when your (protein) partner speeds up…
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Reposted by Ernst Schmid
Online now: A metabolic atlas of mouse aging
A metabolic atlas of mouse aging
Pilley et al. describe how metabolite levels change in 12 organs from male and female mice across five ages, spanning adolescence to old age. They reveal that organs show distinct age- and sex-specific changes in metabolism. They also develop metabolic clocks that predict putative metabolic drivers of aging, including hydroxyproline.
dlvr.it
November 25, 2025 at 4:42 PM
Online now: A metabolic atlas of mouse aging
Reposted by Ernst Schmid
Protein domains have no single definition, so why stick to one segmentation? 🧩
Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing.
You control the granularity. 👇
🔗 doi.org/10.1093/bioi...
Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing.
You control the granularity. 👇
🔗 doi.org/10.1093/bioi...
November 24, 2025 at 4:01 PM
Protein domains have no single definition, so why stick to one segmentation? 🧩
Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing.
You control the granularity. 👇
🔗 doi.org/10.1093/bioi...
Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing.
You control the granularity. 👇
🔗 doi.org/10.1093/bioi...
Reposted by Ernst Schmid
Our lab is seeking a Postdoctoral Fellow. The position is intentionally broad, as we are looking for outstanding researchers from diverse scientific backgrounds to advance our understanding of cilia and ciliopathies: academicpositions.harvard.edu/postings/15526
HMS - Postdoctoral Fellow in BCMP, Brown Lab
We invite applicants for a postdoctoral fellow position in the Brown lab at Harvard Medical School in Boston, Massachusetts. The Brown lab uses structural, biophysical, and biochemical approaches to d...
academicpositions.harvard.edu
November 18, 2025 at 8:05 PM
Our lab is seeking a Postdoctoral Fellow. The position is intentionally broad, as we are looking for outstanding researchers from diverse scientific backgrounds to advance our understanding of cilia and ciliopathies: academicpositions.harvard.edu/postings/15526
No worries and valid point. I probably won’t be involved in future efforts but I know that Johannes is definitely looking to expand efforts. Happy to put you two in touch via email if you’d like.
November 16, 2025 at 2:34 AM
No worries and valid point. I probably won’t be involved in future efforts but I know that Johannes is definitely looking to expand efforts. Happy to put you two in touch via email if you’d like.
Thanks! Through the NSF NAIRR pilot program we were paired with an industry partner to support our AI-related project. The program connected us with NVIDIA and they provided three months of access to a 256-GPU DGX cluster, which is where we ran all of the AlphaFold predictions.
November 14, 2025 at 12:10 AM
Thanks! Through the NSF NAIRR pilot program we were paired with an industry partner to support our AI-related project. The program connected us with NVIDIA and they provided three months of access to a 256-GPU DGX cluster, which is where we ran all of the AlphaFold predictions.
Thanks Pedro! Our nomination procedure used evidence count from BioGRID as one of the features. We didn’t rely on it (or other dbs) exclusively because we wanted to preserve the ability to nominate interaction pairs that may have been missed by existing physical PPI databases.
November 14, 2025 at 12:05 AM
Thanks Pedro! Our nomination procedure used evidence count from BioGRID as one of the features. We didn’t rely on it (or other dbs) exclusively because we wanted to preserve the ability to nominate interaction pairs that may have been missed by existing physical PPI databases.
Thanks to members of rhe @johanneswalter.bsky.social lab and our fantastic collaborators @alanbrownhms.bsky.social and Agata Smogorzewska, we experimentally verified several of these new PPIs. But don’t worry, there are plenty more to work on. Come explore the data and see what you find!
November 12, 2025 at 9:26 PM
Thanks to members of rhe @johanneswalter.bsky.social lab and our fantastic collaborators @alanbrownhms.bsky.social and Agata Smogorzewska, we experimentally verified several of these new PPIs. But don’t worry, there are plenty more to work on. Come explore the data and see what you find!
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
The difference feels like it will be much more informative than overall values.
October 26, 2025 at 5:08 PM
The difference feels like it will be much more informative than overall values.
Reposted by Ernst Schmid
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
Reposted by Ernst Schmid
Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.
September 4, 2025 at 9:55 PM
Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.
Just wanted to say that you making this MSA server available to the community is a true service to humanity. Thank you! Have you considered setting up a donation system? I expect many people would contribute!
August 16, 2025 at 4:32 PM
Just wanted to say that you making this MSA server available to the community is a true service to humanity. Thank you! Have you considered setting up a donation system? I expect many people would contribute!
Reposted by Ernst Schmid
If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.
August 15, 2025 at 5:48 PM
If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.
Reposted by Ernst Schmid
Great talk by @sami-c.bsky.social about the proper use and caveats of AlphaFold2/3 predictions, highly recommended to watch www.youtube.com/watch?v=z7vy...
Structure Prediction and Design using AlphaFold – Sami Chaaban
YouTube video by MRC Laboratory of Molecular Biology
www.youtube.com
August 1, 2025 at 9:53 AM
Great talk by @sami-c.bsky.social about the proper use and caveats of AlphaFold2/3 predictions, highly recommended to watch www.youtube.com/watch?v=z7vy...
Reposted by Ernst Schmid
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
July 22, 2025 at 2:13 PM
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
Reposted by Ernst Schmid
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Our AlphaFold 3 prediction analysis tool is now accepting the new version of the AlphaFold 3 server output files. Thanks to those who let me know about the output change and apologies for any inconvenience! predictomes.org/tools/af3/
Predictomes | AF3 ANALYSIS
A free interactive resource for viewing predicted AlphaFold multimer structures for protein pairs in biological pathways.
predictomes.org
June 23, 2025 at 2:04 PM
Our AlphaFold 3 prediction analysis tool is now accepting the new version of the AlphaFold 3 server output files. Thanks to those who let me know about the output change and apologies for any inconvenience! predictomes.org/tools/af3/
Reposted by Ernst Schmid
Very happy to share that a large part of my thesis work is out today: B. subtilis uses the second messenger c-di-AMP to modulate its turgor pressure in response to the state of its cell envelope. www.nature.com/articles/s41...
Cyclic-di-AMP modulates cellular turgor in response to defects in bacterial cell wall synthesis - Nature Microbiology
Brogan et al. uncover a signalling pathway in which levels of the nucleotide second messenger c-di-AMP increase in response to defects in cell wall synthesis. This regulatory pathway decreases turgor ...
www.nature.com
June 17, 2025 at 12:20 PM
Very happy to share that a large part of my thesis work is out today: B. subtilis uses the second messenger c-di-AMP to modulate its turgor pressure in response to the state of its cell envelope. www.nature.com/articles/s41...
Excited to share that our EndoMap project is now out! A fun collaboration with Miguel Gonzalez-Lozano from the @harperlabhms.bsky.social. Explore our #AlphaFold structural interactome of #XLMS complexes in endosomes-> endomap.hms.harvard.edu
and read about it here->
www.nature.com/articles/s41...
and read about it here->
www.nature.com/articles/s41...
EndoMAP.v1 charts the structural landscape of human early endosome complexes - Nature
A study presents EndoMAP.v1, a resource that combines information on protein interactions and crosslink-supported structural predictions to map the interaction landscape of early endosomes.
www.nature.com
May 28, 2025 at 5:09 PM
Excited to share that our EndoMap project is now out! A fun collaboration with Miguel Gonzalez-Lozano from the @harperlabhms.bsky.social. Explore our #AlphaFold structural interactome of #XLMS complexes in endosomes-> endomap.hms.harvard.edu
and read about it here->
www.nature.com/articles/s41...
and read about it here->
www.nature.com/articles/s41...
Reposted by Ernst Schmid
Last week I learned that all my NIH awards were terminated due to perceived acts of antisemitism by Harvard. My understanding (which may be incorrect) is that this has been extended to literally every grant to grad students, postdocs and faculty throughout the university.
May 21, 2025 at 1:54 AM
Last week I learned that all my NIH awards were terminated due to perceived acts of antisemitism by Harvard. My understanding (which may be incorrect) is that this has been extended to literally every grant to grad students, postdocs and faculty throughout the university.
Reposted by Ernst Schmid
Read all about Apoorva Baluapuri’s new work on Integrator (INT) in HMS News! @baluapuri.bsky.social @adelmanlab.bsky.social
tinyurl.com/y2fx22c2
tinyurl.com/y2fx22c2
What Happens When a Gene Quality-Control Mechanism Fails?
Study solves riddle of how mutations in Integrator complex relate to neurodegeneration, cancer
tinyurl.com
May 6, 2025 at 3:56 PM
Read all about Apoorva Baluapuri’s new work on Integrator (INT) in HMS News! @baluapuri.bsky.social @adelmanlab.bsky.social
tinyurl.com/y2fx22c2
tinyurl.com/y2fx22c2