Excited to share our now published paper @cp-cell.bsky.social highlighting advances in modeling the evolution of protein-protein interactions with MSA Pairformer. Big thanks to Zhidian Zhang, Olivia Tang, @eunbelivable.bsky.social @milot.bsky.social @martinsteinegger.bsky.social and @sokrypton.org!

Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Protein language models have excelled at modeling individual proteins, but extending these capabilities to protein complexes remains a major challenge. MSA Pairformer, a parameter-efficient protein la...

cell.com

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

Something that I am very excited about: the latest version of @chimerax.ucsf.edu (v1.12) now has a cavity analysis function

Amazing paper. A megadalton enzyme complex that: - combines both electron bifurcation AND confurcation steps - has a new type of iron-sulfur cluster - a new kind of weird electron transfer path - super charges electrons to reduce aromatic rings - also powers respiration 😳

Ben Engel@cellarchlab.com · 4mo ago

Across scales from cells🦠 to atoms⚛️ – We reveal how anaerobic #bacteria break down very stable aromatic compounds found e.g. in oil spills 🛢️ #Bioremediation #TeamTomo 🧪 🧶🧬 🔬 Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social

1/ Excited to share our preprint! 🥳 Degradation of aromatic compounds, including BTEX pollutants, requires highly endergonic aromatic ring reduction. Using #cryoEM and in situ #cryoET, we show how BCRII couples electron bifurcation modules in one giant redox machine www.biorxiv.org/content/10.6...

One of biggest mysteries in biology: how did complex eukaryotic cells evolve from simple microbes? ~1.8 billion years ago, an archaeal cell likely merged with a bacterium to form the first eukaryotic cell, but can we ever find direct evidence of this transformative event? 🦠 🚶‍♂️

Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...

Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments

Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...

journals.plos.org

Found out today that @kyclark.bsky.social has made their great 'Mastering Python for Bioinformatics' book into a YouTube series. youtube.com/playlist?lis...

Mastering Python for Bioinformatics - YouTube

Mastering Python for Bioinformatics (O'Reilly, 2022) by Ken Youens-Clark demonstrates how to write effective Python code and how to use tests to write and re...

youtube.com

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk

This has been up for a while but I haven’t really publicized it. Introducing ciMIST: sparse, self-consistent network models of local and global protein conformational entropy, learned from molecular dynamics. This helps with analyzing MD and connecting to experiments www.biorxiv.org/content/10.1...

Having a hard time keeping up with the fast-moving field of origin of eukaryotes/Asgards archaea? Our new perspective article can help, we review the status of research over the last decade and where it's going. The archaeal roots of eukaryotic life www.pnas.org/doi/10.1073/...

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

“Some have even argued that private funding is superior, maintaining that it is more flexible, less prone to groupthink, and reduces the “burden” on taxpayers. But can the private sector really replace public funding? History suggests not” www.science.org/doi/10.1126/...

Private money cannot replace public funding of science

Who should pay for American science? In the current political climate, many are looking to the private sector to compensate for cuts in public funding. At the Harvard School of Public Health—particula...

science.org

A minimal PyTorch re-implementation of AlphaFold2 github.com/ChrisHayduk/... We need more stuff like this. The incentive is to always be making the new groundbreaking tool, while maintenance + improvement of "old" tools gets left behind. But there is still heaps to be gained in "old" tools

Aerobic syngas conversion: opportunities, challenges, and solutions www.sciencedirect.com/science/arti...

Any paper that quotes Italo Calvino is an instant 10/10 in my book 'An Interpretation, Survey, and Outlook of Microbial Macroecology' by @shoestrapped.bsky.social ecoevorxiv.org/repository/v...

Insects were my first scientific love (before I knew about proteins). So I love hearing about some new weird insect "Temnothorax kinomurai is the first ant species known to lack both workers and males and to consist exclusively of queens" doi.org/10.1016/j.cu... @currentbiology.bsky.social

Understanding how enzymes work: the journey to ensemble–function studies febs.onlinelibrary.wiley.com/doi/10.1111/... This is an exceptionally well written review on how enzymes work. Rather than the structure-function relationship, Herschlag & Du analyse the ensemble-function relationship

Structural ontogeny of protein-protein interactions: www.science.org/doi/10.1126/... Fundamental work on how PPIs (co)evolve, combining directed evolution and machine learning to reveal the role of chance and contingency.

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n doi.org/10.64898/202...

You go, Katy! 🚀 I’m so proud of you, and so happy to finally see this in its final form! Count me in on your corner to keep on cheering for you! Looking forward to doing more amazing science together 💪 Check @katyappler.bsky.social thread below for highlights and the full paper here: rdcu.be/e4A70

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature

Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...

nature.com

Kathryn (Katy) Appler@katyappler.bsky.social · 6mo ago

Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12

Asgard archaeal origin of microtubules: www.biorxiv.org/content/10.6...

I present this extremely niche meme for the hydrogenase community

"GenAI increases output and helps programmers expand into new domains—but only for senior- level developers. Early-career developers, despite being the most enthusiastic adopters, see no measurable gains" www.science.org/doi/10.1126/...

Who is using AI to code? Global diffusion and impact of generative AI

Generative coding tools promise big productivity gains, but uneven uptake could widen skill and income gaps. We train a neural classifier to spot artificial intelligence (AI)–generated Python function...

science.org

Our work is published today: ‘Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor’. This was a huge effort lead by @katyappler.bsky.social. Extremely grateful to have been a part of this amazing project! 😊🦠🧬 Links: www.nature.com/articles/s41... www.nature.com/articles/s41...

Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...

One of the biggest questions in biology is how complex cells evolved about 2 billion years ago. Here's my new story on how scientists are solving the mystery of eukaryotes like us. Gift link: nyti.ms/4qMbo22

At long last! Check out the link to our publication in @nature.com to learn more. doi.org/10.1038/s415... 12/12

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature

Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...

doi.org

New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...