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

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.

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...

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".

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

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/

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...

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.

Read all about Apoorva Baluapuri’s new work on Integrator (INT) in HMS News! @baluapuri.bsky.social @adelmanlab.bsky.social tinyurl.com/y2fx22c2

 🧬🎉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...

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... 🧵🧪

How do cells achieve an optimal mitochondrial distribution? Excited to share a piece of this puzzle: www.science.org/doi/10.1126/...

🔬 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

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).

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.

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

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!

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

🧬 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

🚀 #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

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...

See your DNA sequences straight in the results email 🤘 Are we the first to do this? Let us know!

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

AlphaMove xkcd.com/3045

Our story on the mechanism of co-transcriptional histone mark deposition is now officially out: www.science.org/doi/10.1126/...

Cells are filled with toxic stuff that damages healthy proteins. Is that garbage just left to rot on the curb? No way! Ubiquitin ligases have evolved to recognize chemical damage and clean it up! www.nature.com/articles/s41...

An update to #AlphaFold3 server. Now, you can add any ligand from the PDB using a CCD Code (up to 2024_10_28). Here is an MPro #SARS-CoV2 inhibitor from PDB 8u9h. The crystal structure is grey, and the #AF3 model is colored by pLDDT.

Stem cell-like states confer poor outcomes in blood cancer—but what mechanisms drive this and how can they be therapeutically targeted? In our new preprint, we show how a single TF represses one enhancer to maintain a subset of high-risk leukemias: 🧵👇 www.biorxiv.org/content/10.1...

🙏 🙏 Honored to have the work from @tjflemin.bsky.social from our lab featured in the Best of #ASH24!!!

The NVIDIA holiday sweater this year with DNA and small molecules on it! 🧬✨

TTF2 promotes replisome eviction from stalled forks in mitosis https://www.biorxiv.org/content/10.1101/2024.11.30.626186v1

We ran a complete in-silico protein interaction screen of the monkeypox proteome using AlphaFold. Have a look at the interactive PPI network at www.poxfolds.org/poxppis.php All data is open source and can also be downloaded at zenodo