Ernst Schmid
@ernstschmid.bsky.social
Full stack developer who occasionally wears a lab coat. Graduate student at Harvard Medical School.
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
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
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.
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
Reposted by Ernst Schmid

🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...
🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...
May 6, 2025 at 3:08 PM

🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...
🧬🎉Thrilled to share our new chromatin remodeling study! We reveal three states of human CHD1 and identify a novel "anchor element" that interacts with the acidic patch—conserved among remodelers. Our structures clarify mechanisms of remodeler recruitment! Link: authors.elsevier.com/a/1l2ik3vVUP...
Reposted by Ernst Schmid
Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
🧵🧪
🧵🧪
Zero-shot design of drug-binding proteins via neural selection-expansion
Computational design of molecular recognition remains challenging despite advances in deep learning. The design of proteins that bind to small molecules has been particularly difficult because it requ...
www.biorxiv.org
April 28, 2025 at 3:22 PM
Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1...
🧵🧪
🧵🧪
Reposted by Ernst Schmid
How do cells achieve an optimal mitochondrial distribution? Excited to share a piece of this puzzle: www.science.org/doi/10.1126/...
ARMC1 partitions between distinct complexes and assembles MIRO with MTFR to control mitochondrial distribution
ARMC1 partitions between distinct outer mitochondrial membrane complexes and the cytosol to control mitochondrial distribution.
www.science.org
April 10, 2025 at 2:49 PM
How do cells achieve an optimal mitochondrial distribution? Excited to share a piece of this puzzle: www.science.org/doi/10.1126/...
Reposted by Ernst Schmid
🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome
April 6, 2025 at 9:45 AM
🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome
Reposted by Ernst Schmid
It has been coming a long way... happy to share our latest work with you: www.biorxiv.org/content/10.1...
Here, we show the importance of septal fortification by the Class A Penicillin Binding Protein, PBP1b, in E. coli and provide a molecular mechanism for this function. (1/12).
Here, we show the importance of septal fortification by the Class A Penicillin Binding Protein, PBP1b, in E. coli and provide a molecular mechanism for this function. (1/12).
The aPBP-type cell wall synthase PBP1b plays a specialized role in fortifying the Escherichia coli division site against osmotic rupture
A multi-protein system called the divisome promotes bacterial division. This apparatus synthesizes the peptidoglycan (PG) cell wall layer that forms the daughter cell poles and protects them from osmo...
www.biorxiv.org
April 3, 2025 at 10:13 PM
It has been coming a long way... happy to share our latest work with you: www.biorxiv.org/content/10.1...
Here, we show the importance of septal fortification by the Class A Penicillin Binding Protein, PBP1b, in E. coli and provide a molecular mechanism for this function. (1/12).
Here, we show the importance of septal fortification by the Class A Penicillin Binding Protein, PBP1b, in E. coli and provide a molecular mechanism for this function. (1/12).
Reposted by Ernst Schmid
Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.
March 27, 2025 at 8:15 AM
Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.
Reposted by Ernst Schmid
I think @nytimes.com Spelling Bee needs some Bio101. It also rejects intron, allele (and derivations), and actin. At least it has gene.
March 26, 2025 at 10:36 AM
I think @nytimes.com Spelling Bee needs some Bio101. It also rejects intron, allele (and derivations), and actin. At least it has gene.
Reposted by Ernst Schmid
What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!
March 23, 2025 at 12:14 PM
What an amazing experience to be at the 76th Mosbacher kolloquim! Awesome talks on protein design and structural biology and a lot of conceptual discussions on where the field is going. Glad to also have been able to present our poster on binder design using BindCraft!
Reposted by Ernst Schmid
Thank you so much for integrating Foldseek into the great ChimeraX.
March 7, 2025 at 8:47 AM
Thank you so much for integrating Foldseek into the great ChimeraX.
Reposted by Ernst Schmid
🧬 Exciting AlphaFold DB updates:
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
March 4, 2025 at 6:18 PM
🧬 Exciting AlphaFold DB updates:
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
✅ Bulk downloads – Up to 100 structures (PDB, mmCIF / JSON)
✅ pLDDT filtering – Find high-confidence models
✅ Table exports
📖 Read
www.sciencedirect.com/science/arti...
🔗 Explore
alphafold.ebi.ac.uk
#AlphaFold #AI #Bioinformatics #ProteinStructures
Reposted by Ernst Schmid
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social