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Reposted by James Lingford

Ulad Litvin @ulad-litvin.bsky.social · 12d

Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵

📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk

Viro3D: a comprehensive database of virus protein structure predictions | Molecular Systems Biology

imageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i...

doi.org

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James Lingford @jameslingford.bsky.social · 20d

RFdiffusion3 is here: www.biorxiv.org/content/10.1...

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James Lingford @jameslingford.bsky.social · 21d

Switched from using pandas to @pola.rs and it has been a total life saver. Handling dataframes is way more intuitive with the method chaining syntax. Prettier terminal printing, better error messages, lightning fast, fewer headaches.

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James Lingford @jameslingford.bsky.social · Sep 2

Recent advances in the inference of deep viral
evolutionary history journals.asm.org/doi/10.1128/...

A review on structural phylogenetics utility and limitations

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James Lingford @jameslingford.bsky.social · Sep 1

Fantastic review on methodological developments in protein structural phylogenetics
academic.oup.com/gbe/article/...

Protein Structural Phylogenetics

Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his

academic.oup.com

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James Lingford @jameslingford.bsky.social · Aug 27

Large protein databases reveal structural complementarity and functional locality
www.nature.com/articles/s41...

Large protein databases reveal structural complementarity and functional locality - Nature Communications

Researchers mapped the protein structure landscape, revealing structural complementarity across databases and functional clustering in specific regions. Their web tool helps explore this space, unlock...

www.nature.com

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Reposted by James Lingford

Indrek Kalvet @ikalvet.bsky.social · Aug 22

RFdiffusion2 is now live!
github.com/RosettaCommo...

You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!

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James Lingford @jameslingford.bsky.social · Aug 21

This is a remarkable paper on protein evolution from the Lehner lab. What makes it especially cool is that all the code to reproduce all the analysis/plots is included in Jupyter notebooks up on Github
www.science.org/doi/10.1126/...
github.com/lehner-lab/c...

GitHub - lehner-lab/combinatorialcores: Source code for analyses and figure reproduction in "Genetics, energetics, and allostery in proteins with randomized cores and surfaces", Escobedo et. al Scienc...

Source code for analyses and figure reproduction in "Genetics, energetics, and allostery in proteins with randomized cores and surfaces", Escobedo et. al Science 2025 - lehner-lab/combina...

github.com

James Lingford @jameslingford.bsky.social · Aug 13

• a big concern I have with these LLMs is how they might end up changing our attitudes around productivity. The promise is instant results & faster publications. But the cost will end up being garbage results that are only caught when it's too late

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James Lingford @jameslingford.bsky.social · Aug 13

Just to piggyback on this critique of LLMs for coding with some of my own critiques:

• it's a bad idea to install a tool on your machine that has vast read+write permissions
• code that works but is really outputting false info is a real danger and hard to catch. LLMs make that danger worse

Will Ratcliff @wcratcliff.bsky.social · Aug 12

Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.

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James Lingford @jameslingford.bsky.social · Aug 11

Does sequence clustering confound AlphaFold2?
www.sciencedirect.com/science/arti... From @hkws.bsky.social

Does sequence clustering confound AlphaFold2?

Predicting multiple conformational states of proteins represents a significant open challenge in structural biology. Increasingly many methods have be…

www.sciencedirect.com

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Reposted by James Lingford

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Aug 5

MMseqs2 v18 is out
- SIMD FW/BW alignment (preprint soon!)
- Sub. Mat. λ calculator by Eric Dawson
- Faster ARM SW by Alexander Nesterovskiy
- MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API)
💾 github.com/soedinglab/M... & 🐍

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James Lingford @jameslingford.bsky.social · Jul 23

Pretty amazing looking tool for analysing genetic neighbourhoods:
github.com/chevrettelab...

GitHub - chevrettelab/gator-gc

Contribute to chevrettelab/gator-gc development by creating an account on GitHub.

github.com

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Reposted by James Lingford

Maciek Wiatrak @macwiatrak.bsky.social · Jul 21

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

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Reposted by James Lingford

Kassiani Panagiotou @kassipan.bsky.social · Jul 20

Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.

The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

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Reposted by James Lingford

Zeqian Li @zeqianli.bsky.social · Jul 19

New tgv release: local cache!

tgv download hg38

Download UCSC reference genomes to a local sqlite db for much faster browsing. Awesome Rust tools (twobit, bigtools) made this simple.

github.com/zeqianli/tgv

GitHub - zeqianli/tgv: Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

github.com

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Reposted by James Lingford

Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

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James Lingford @jameslingford.bsky.social · Jul 11

Got this setup working where I can now run .ipynb notebooks right from inside the terminal with a combination of neovim, quarto, kitty, and this neovim plugin called molten: github.com/benlubas/mol...
Never have to abandon my precious vim setup again

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Reposted by James Lingford

Rhys Grinter @rhyswg.bsky.social · Jul 9

Excited to share our latest work using AI-designed proteins to block heme-piracy by E. coli. Published in @natcomms.nature.com. A team effort between my lab and the ‪‪@knottrna.bsky.social‬ ‬lab, with experimental work led by the talented @danielrfox.bsky.social
www.nature.com/articles/s41...

Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins - Nature Communications

Many pathogens encode transporters that extract heme directly from host proteins. In this study, the authors demonstrate the utility of de novo-designed proteins in understanding the mechanism behind ...

www.nature.com

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James Lingford @jameslingford.bsky.social · Jul 7

Been eagerly awaiting this one. Amazing work

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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Reposted by James Lingford

Martin Pacesa @martinpacesa.bsky.social · Jun 30

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!

github.com/martinpacesa...

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James Lingford @jameslingford.bsky.social · Jun 27

Some matplotlib work in progress

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Reposted by James Lingford

Will Ratcliff @wcratcliff.bsky.social · Jun 24

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

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James Lingford @jameslingford.bsky.social · Jun 24

Closer... I think at this point the solution lies in manually making a list of the hex codes, but that's for another day.

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James Lingford @jameslingford.bsky.social · Jun 23

Revisiting this topic now that I've forced myself to use PyMOL. Using this script to install the viridis family of colour palettes: github.com/smsaladi/pym... and running '"spectrum count, palette=magma, MODEL_NAME". The palette is not there still. They must modify the magma palette somehow

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