jameslingford.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

I love it

submitted 2 days ago • 0 comments

Baker lab PyMOL config 👇

submitted 2 days ago • 0 comments

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

submitted 3 days ago • 0 comments

AFESM: 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...

submitted 4 days ago • 4 comments

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...

submitted 11 days ago • 0 comments

AlphaFold 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...

submitted 13 days ago • 3 comments

GTDB Release 10-RS226 (16th April 2025) has been published gtdb.ecogenomic.org

submitted 13 days ago • 1 comment

Made my terminal colours pretty, so now I'm a true hacker 😎

submitted 13 days ago • 1 comment

Extremely useful guide on how to do Bash-like things inside Python. github.com/ninjaaron/re...

submitted 14 days ago • 0 comments

I'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...

submitted 14 days ago • 1 comment

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

submitted 15 days ago • 3 comments

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?)

submitted 15 days ago • 3 comments

Crash course in MD-sim today 💻

submitted 20 days ago • 0 comments

Our 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...

submitted 26 days ago • 0 comments

Screwed up my Linux machine by trying to be clever. So here we go again with a fresh install

submitted 24 days ago • 0 comments

Microtubules in Asgard archaea www.cell.com/cell/fulltex...

submitted 28 days ago • 0 comments

Short blog post from me: converting MMseqs2 clusters to split fasta files www.jameslingford.com/blog/mmseqs-...

submitted 29 days ago • 0 comments

Gene synthesis is often the most expensive part of protein engineering with generative models. Happy to have played a small part in this work, where Chase developed a method for precision library construction at scale, with per-gene costs as low as $1.50. @philromero.bsky.social

submitted 37 days ago • 1 comment

🚧Check out the preprint of a story I was involved in, lead by Lars Schäfer and Thomas Happe 🚧 We found that an additional cysteine in [FeFe]-hydrogenase enhances the flexibility of a conserved loop and facilitates the formation of an O2-insensitive cofactor state. www.biorxiv.org/content/10.1...

submitted 41 days ago • 1 comment

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

submitted 43 days ago • 1 comment

Metabuli-App simplifies (meta)genomic taxonomic analysis. Classify sequences, explore results interactively, create/update DBs & more. Runs on Windows, Linux & Mac. 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla... Sankey plot available as a own component 💾 github.com/steineggerla...

submitted 43 days ago • 0 comments

Thrilled to share the structure of dimerised human PINK1 docked to an endogenous translocase array on the mitochondrial surface, composed of two TOM complexes, bridged by a VDAC2 dimer! Published today in Science www.science.org/doi/10.1126/... @wehi-research.bsky.social @komanderlab.bsky.social

submitted 48 days ago • 9 comments

Great to see all the #standupforscience protests from my American colleagues. Never give up

submitted 54 days ago • 0 comments

Very proud to share our latest work from the lab. Together with @kailalab.bsky.social and Müller Lab. We found such an elegant mechanism - Charge follows charge. The positive Na+ follows the negative electron across the membrane and back. rdcu.be/ecCmr

submitted 54 days ago • 0 comments

I've been praying for this crossover

submitted 54 days ago • 0 comments

Now that's one damn good summary video

submitted 58 days ago • 0 comments

One more for the reading list: Computational protein design [review] www.nature.com/articles/s43...

submitted 59 days ago • 0 comments

New isolates from eukaryote's closest archaeal relative: ‘Hodarchaeales’!! Syntrophic microaerotolerant peptide-degrading anaerobic archaea w/ simple cell structure & protrusions. Features conserved across the phylum provide new insight into our ancestor’s biology! www.biorxiv.org/content/10.1...

submitted 63 days ago • 8 comments

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

submitted 68 days ago • 2 comments

A response from Wayment-Steele. www.biorxiv.org/content/10.1...

submitted 68 days ago • 0 comments

Turns out AF-Cluster does not sample different evolutionary couplings. The prediction of fold-switched states is likely due to AF2 memorisation of its training set www.nature.com/articles/s41...

submitted 69 days ago • 1 comment

I'll post more about this later. But for a long time, we've observed odd behavior of AlphaFold's ipTM in the presence of disorder and accessory domains. Looking into the math points a way to solving the problem. There are other solutions besides ours. But I think understanding the math is key.

submitted 75 days ago • 0 comments

We are happy to share that the code and weights of PLACER (formerly known as ChemNet) are now public! This method allows for rapid evaluation of protein side chain and ligand conformational ensembles, with uses in ligand docking and enzyme evaluation. github.com/baker-labora...

submitted 76 days ago • 1 comment

Goodbye @lorneproteins.bsky.social 2025, and thanks for the great conference. I'll miss getting to see hundreds of cockatoos whenever I step outside

submitted 77 days ago • 0 comments

Mounting evidence that the [4Fe-4S] cluster of the [FeFe]-hydrogenase active site cofactor is more complex than your ordinary cubane... Exploiting advanced EPR spectroscopy, Mügge and her team uncovered distinct valence states (via @angewandtechemie.bsky.social) 🟡🔴 doi.org/10.1002/anie... #chemsky

submitted 99 days ago • 2 comments

Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work www.biorxiv.org/content/10.1...

submitted 107 days ago • 0 comments

Hydrogen Energy System That Uses [NiFe] Hydrogenase Functional Models and Works at 20–40 °C pubs.acs.org/doi/full/10.... Neat idea for hydrogen fuel --> use an electron carrier which is easier to store and transport than H2 gas, and then produce H2 gas with hydrogenases when needed

submitted 109 days ago • 0 comments

New method to help with protein function prediction when mining proteomes with AlphaFold www.nature.com/articles/s41...

submitted 109 days ago • 0 comments