James Lingford
PhD student in structural biology with @greening.bsky.social and @knottrna.bsky.social at Monash Uni. (he/him)
Interested in hydrogenases, evolution, protein design.
💻 jameslingford.com
- Reposted by James Lingford[Not loaded yet]
- Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
- Reposted by James LingfordExcited 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.
- Reposted by James LingfordViro3D 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...
- Reposted by James LingfordRFdiffusion2 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
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- Pretty amazing looking tool for analysing genetic neighbourhoods: github.com/chevrettelab...
- Reposted by James Lingford💥 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[Not loaded yet]
- Reposted by James LingfordOut 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
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- Been eagerly awaiting this one. Amazing work
- 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
- Reposted by James LingfordWe 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
- Reposted by James Lingford1/27 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".
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- Learning some Blender molecular nodes from @sarahjpiper.bsky.social @ccemmp-outreach.bsky.social
- Reposted by James LingfordNew 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.
- Reposted by James LingfordI'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.
- Reposted by James Lingford
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...
- Reposted by James LingfordWhy 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/...
- Reposted by James LingfordNIH 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!
- Reposted by James LingfordOn 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...
- Reposted by James LingfordYou 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 !
- Hey #TeamTomo, Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging? That's why @florentwaltz.bsky.social and I made this website! tomoguide.github.io Follow the thread 1 /🧵 #CryoET #CryoEM 🔬🧪
- Reposted by James LingfordNew 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.
- A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome biorxiv.org/content/10.1101/202…
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- Absolutely catastrophic for science
- Nature reports that the National Science Foundation has stopped awarding new grants and allotting funds to existing ones. All of them. @colincarlson.bsky.social says that unless the freeze is lifted, it “is going to destroy people's labs.” 2/10 www.nature.com/articles/d41...
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- 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...
- Reposted by James LingfordAFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
- ChimeraX tip: to get a lined border around an internal surface requires superposing two separate copies of your model. One for showing the surrounding cartoon structure, and the other showing just the surface (and select that one to give it a border) www.jameslingford.com/blog/chimera...
- Reposted by James LingfordAlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...
- AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2 biorxiv.org/content/10.1101/202…
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- Made my terminal colours pretty, so now I'm a true hacker 😎
- Extremely useful guide on how to do Bash-like things inside Python. github.com/ninjaaron/re...
- Reposted by James LingfordI'm truly excited to announce our new publication in @nature.com unraveling a central picture of the Methyl-coenzyme M reductase (MCR) activation machinery and it's strong ATP dependency - kudos to @rnfr2d2.bsky.social for the fantastic illustration! LINK: www.nature.com/articles/s41...
- Close to recreating it in ChimeraX: 1. Install the python file: github.com/smsaladi/chi... 2. rainbow palette magma 3. col modify #1 blackness - 40 4. col modify #1 whiteness - 40 5. col modify #1 saturation - 50 6. col modify #1 lightness + 20 Room for improvement, needs more desaturation
- Something I've been wondering is what sort of settings the Baker lab is using to get these gorgeous PyMOL figures with? (I'm assuming it's PyMOL?)
- Crash course in MD-sim today 💻
- Reposted by James LingfordOur work on HIV-1 matrix, led by James Stacey and @dhrebik.bsky.social, is in this week's @nature.com. Extended explanatory video from @margotriggi.bsky.social. www.nature.com/articles/s41...
- Screwed up my Linux machine by trying to be clever. So here we go again with a fresh install
- Microtubules in Asgard archaea www.cell.com/cell/fulltex...
- Short blog post from me: converting MMseqs2 clusters to split fasta files www.jameslingford.com/blog/mmseqs-...
- Reposted by James Lingford[Not loaded yet]
- Reposted by James Lingford[Not loaded yet]
- Hydrogenase-driven ATP synthesis from air www.biorxiv.org/content/10.1... New work from us where we put the Huc hydrogenase to work to see if it can generate a proton motive force. It can! cc: @ashleighkropp.bsky.social @rhyswg.bsky.social @greening.bsky.social
