Lightnews — Scholar-powered news

Reposted by Ernst Schmid

Lucas Farnung @lucas.farnunglab.com · Sep 4

Martin Filipovski successfully defended his PhD thesis today! Congrats, Dr. Filipovski.

The Farnung Lab celebrates Martin Filipovski's thesis defense.

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Ernst Schmid @ernstschmid.bsky.social · Aug 16

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!

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Reposted by Ernst Schmid

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Aug 15

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.

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Reposted by Ernst Schmid

Martin Pacesa @martinpacesa.bsky.social · Aug 1

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

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Reposted by Ernst Schmid

Pedro Beltrao @pedrobeltrao.bsky.social · Jul 22

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".

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Reposted by Ernst Schmid

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 7

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

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Ernst Schmid @ernstschmid.bsky.social · Jun 23

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

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Reposted by Ernst Schmid

anna brogan @apbrogan.bsky.social · Jun 17

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

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Ernst Schmid @ernstschmid.bsky.social · May 28

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...

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

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Reposted by Ernst Schmid

Joe Loparo @joeloparo.bsky.social · May 21

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.

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Reposted by Ernst Schmid

Harvard Med BCMP @hms-bcmp.bsky.social · May 6

Read all about Apoorva Baluapuri’s new work on Integrator (INT) in HMS News! @baluapuri.bsky.social @adelmanlab.bsky.social
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

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Reposted by Ernst Schmid

Lucas Farnung @lucas.farnunglab.com · May 6

🧬🎉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...

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Reposted by Ernst Schmid

Nick Polizzi @nickpolizzi.bsky.social · Apr 28

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

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Reposted by Ernst Schmid

Susan Shao @sshaolab.bsky.social · Apr 10

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

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Reposted by Ernst Schmid

Lucas Farnung @lucas.farnunglab.com · Apr 6

🔬 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

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Reposted by Ernst Schmid

Andrea Vettiger @avettiger.bsky.social · Apr 3

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).

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

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Reposted by Ernst Schmid

jankosinski.bsky.social @jankosinski.bsky.social · Mar 27

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.

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Reposted by Ernst Schmid

Brian Plosky @brianplosky.bsky.social · Mar 26

I think @nytimes.com Spelling Bee needs some Bio101. It also rejects intron, allele (and derivations), and actin. At least it has gene.

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Reposted by Ernst Schmid

Martin Pacesa @martinpacesa.bsky.social · Mar 23

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!

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Reposted by Ernst Schmid

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Mar 7

Thank you so much for integrating Foldseek into the great ChimeraX.

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Reposted by Ernst Schmid

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Mar 4

🧬 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

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Reposted by Ernst Schmid

EMBL-EBI @ebi.embl.org · Mar 3

🚀 #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

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Ernst Schmid @ernstschmid.bsky.social · Feb 26

Thanks Andrew!

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Ernst Schmid @ernstschmid.bsky.social · Feb 26

In our tests, SPOC outperforms other commonly used metrics in prioritizing biologically relevant interactions in large scale AF-M screens. We used SPOC to score ~40,000 binary pairs across ~300 genome maintenance proteins. View all data and use SPOC on: predictomes.org

Predictomes | Home

A free interactive resource for viewing predicted AlphaFold multimer structures for protein pairs in biological pathways.

predictomes.org

Ernst Schmid @ernstschmid.bsky.social · Feb 26

Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...

Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions

Schmid and Walter train a classifier that discerns functionally relevant structure predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer, and they use this co...

www.cell.com

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