For fun, I thought I'd compare different AlphaFold softwares on a random sample of 1000 proteins I'm working on. AlphaFold2/ColabFold is still the most accurate, but slowest and most buggy (the run randomly stopped at the 975th protein). Boltz is the best for speed.

Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

As much as I like making plots with matplotlib and seaborn, the way repositioning legends/colourbars works is super unintuitive and a massive timesink.

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

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

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.

Recent advances in the inference of deep viral evolutionary history journals.asm.org/doi/10.1128/... A review on structural phylogenetics utility and limitations

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

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

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!

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...

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

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

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... & 🐍

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

💥 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

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

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

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 🧵

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

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...

Been eagerly awaiting this one. Amazing work

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...

Some matplotlib work in progress

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....

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

Seen similar things where the PAEs of a multimer are poor until all the subunits in the correct stoichiometry are provided. This worries me, because one could have a good prediction like "C", but miss out on the best prediction "D".

Physics-based design of efficient Kemp eliminases @lynnkamerlin.bsky.social www.nature.com/articles/s41...

Learning some Blender molecular nodes from @sarahjpiper.bsky.social @ccemmp-outreach.bsky.social

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

Little shell scripting solution to the problem of finding a group A in column1 of a table that is entirely made up of group B in column2, and sorting for the biggest homogeneous grouping.

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

Proud to present the lab's latest work. The full structure of the sodium translocating methyltransferase (Mtr) bound to a small oxygen-responsive small protein MtrI. Work by Tristan and together with @schmitzstreitslab.bsky.social . www.biorxiv.org/content/10.1101/2025.06.02.657420v1

I'm sick of typing "conda activate ENV" or "conda deactivate" to switch virtual environments. Now I've added a conda/mamba env switcher function that uses fzf to my ~/.zshrc.

Quick blogpost on how to convert the Genome Taxonomy Database (GTDB) protein faa reps into a DIAMOND database that includes taxonomic information and genome ID's www.jameslingford.com/blog/gtdb-to...

Why make a cofactor when you can get it for free? Our work, led by @fabianmunder.bsky.social, shows that bacteria from 22 phyla use the high-affinity transporter PqqU to obtain the redox cofactor PQQ from the environment as an alternative to cofactor synthesis. www.science.org/doi/10.1126/...

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Awk command to unwrap wrapped lines in fasta files. It's just neat!

On this day, 10 years ago, my lab published the @nature.com paper reporting the discovery of the Asgard archaea (Lokiarchaeota at the time), revealing the archaeal nature of eukaryotic cells, and reshaping the Tree of Life. What a ride it has been since then... www.nature.com/articles/nat...

Very much agree with this call to action. Important for scientists to speak out together against all forms of tyranny, and not just speak out against funding cuts. Though I realise that's easy for me to say, since I don't live in the U.S. www.nature.com/articles/d41...

Bioenergetics and the evolution of cellular traits [review]: doi.org/10.1146/annu...

You want to start tomography? Solve structures inside cells? Reach Nyquist 😳 ? @phaips.vd.st and I have a website for you! tomoguide.github.io You'll find a tutorial on how to reconstruct tomograms, pick particles and do subtomogram averaging, using different software! Hope it will be useful !

New paper out! We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp! Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive. It also represents a novel, deep-branching lineage in the archaeal tree.

Peters & Rauegi explore the properties that allow tuning biological FeS cluster reduction potentials (via J. phys. Chem. Lett.) doi.org/10.1021/acs....

Absolutely catastrophic for science

In this new publication, we took #archaea for a walk in the chemical garden 😉. The abiotic hydrogen produced in this setting can fuel M. jannaschii’s metabolism. Great interdisciplinary collaboration with the Orsi lab who initiated and led this study. More here www.nature.com/articles/s41...

I love it

Baker lab PyMOL config 👇

Reading old papers is cool because you never see this sort of casual tone anymore. www.sciencedirect.com/science/arti...