James Lingford
@jameslingford.bsky.social
PhD student in structural biology with @greening.bsky.social and @knottrna.bsky.social at Monash Uni. (he/him)
Interested in hydrogenases, evolution, protein design.
💻 https://www.jameslingford.com/
Interested in hydrogenases, evolution, protein design.
💻 https://www.jameslingford.com/
Reposted by James Lingford
The Elsevier investigation mentioned was initiated after a STAT news piece on the problem, co-authored with Cathryn, @dsamorod.bsky.social, @stairwaytokevin.bsky.social, @jedidiahcarlson.com, @jameslingford.bsky.social and @jowiph.bsky.social
www.statnews.com/2024/06/20/r...
www.statnews.com/2024/06/20/r...
Journals that published Richard Lynn's racist 'research' articles should retract them
Richard Lynn's work has been repeatedly condemned for using flawed methodology and deceptively collated data to support racism. It's past time to retract the studies.
www.statnews.com
November 26, 2025 at 3:33 PM
The Elsevier investigation mentioned was initiated after a STAT news piece on the problem, co-authored with Cathryn, @dsamorod.bsky.social, @stairwaytokevin.bsky.social, @jedidiahcarlson.com, @jameslingford.bsky.social and @jowiph.bsky.social
www.statnews.com/2024/06/20/r...
www.statnews.com/2024/06/20/r...
Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
October 27, 2025 at 2:14 AM
Super cool talk from @kmichie.bsky.social. Lots of examples of how AlphaFold3 does weird stuff
Reposted by James Lingford
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!
October 26, 2025 at 10:40 PM
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.
October 21, 2025 at 9:54 PM
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 Lingford
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
📑 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
September 26, 2025 at 2:06 PM
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
📑 Paper doi.org/10.1038/s443...
🔭 Explore virosphere viro3d.cvr.gla.ac.uk
RFdiffusion3 is here: www.biorxiv.org/content/10.1...
September 19, 2025 at 7:56 AM
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.
September 18, 2025 at 2:21 AM
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
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
September 2, 2025 at 10:35 PM
Recent advances in the inference of deep viral
evolutionary history journals.asm.org/doi/10.1128/...
A review on structural phylogenetics utility and limitations
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/...
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
September 1, 2025 at 11:15 PM
Fantastic review on methodological developments in protein structural phylogenetics
academic.oup.com/gbe/article/...
academic.oup.com/gbe/article/...
Large protein databases reveal structural complementarity and functional locality
www.nature.com/articles/s41...
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
August 27, 2025 at 7:49 AM
Large protein databases reveal structural complementarity and functional locality
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Lingford
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!
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!
August 22, 2025 at 12:51 AM
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!
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...
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
August 21, 2025 at 12:52 AM
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...
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
• 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
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.
August 13, 2025 at 11:38 PM
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
• 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
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
August 11, 2025 at 2:11 AM
Does sequence clustering confound AlphaFold2?
www.sciencedirect.com/science/arti... From @hkws.bsky.social
www.sciencedirect.com/science/arti... From @hkws.bsky.social
Reposted by James Lingford
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... & 🐍
- 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... & 🐍
August 5, 2025 at 8:25 AM
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... & 🐍
- 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...
github.com/chevrettelab...
GitHub - chevrettelab/gator-gc
Contribute to chevrettelab/gator-gc development by creating an account on GitHub.
github.com
July 23, 2025 at 4:37 AM
Pretty amazing looking tool for analysing genetic neighbourhoods:
github.com/chevrettelab...
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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
July 21, 2025 at 9:56 AM
💥 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
Preprint 📝: biorxiv.org/content/10.1...
🧵 1/n
Reposted by James Lingford
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
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
July 20, 2025 at 4:58 PM
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
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
Reposted by James Lingford
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
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
July 19, 2025 at 11:37 PM
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
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
Reposted by James Lingford
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 🧵
July 16, 2025 at 9:59 PM
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
Never have to abandon my precious vim setup again
July 11, 2025 at 7:29 AM
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
Never have to abandon my precious vim setup again
Reposted by James Lingford
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...
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
July 9, 2025 at 11:55 PM
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...
www.nature.com/articles/s41...
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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:45 AM
Been eagerly awaiting this one. Amazing work
Reposted by James Lingford
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...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
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...
github.com/martinpacesa...
Some matplotlib work in progress
June 27, 2025 at 7:13 AM
Some matplotlib work in progress