SPLICECRAFT v1.0 IS LIVE!!!!!!!!!!!!
Open your terminal and type in "pipx install splicecraft" if you want to try it out, then spam "splicecraft update" often as I push updates frequently. A labor of love for the community I adore. Enjoy! 💚
Nature research paper: Epigenetic memory of colitis promotes tumour growth
go.nature.com/4t3apvK
Sebastian S. Cocioba
Essays in Biochemistry publishes themed issues looking at interesting, timely and relevant subjects from across the molecular biosciences. Interested in leading a themed issue? Then fill out our proposal form.🧪 https://ow.ly/xrh050XNAvV
Nature
Happy to have this collaborative work with Zach Armstrong now out in Angewandte chemie doi.org/10.1002/anie... .
We use a linked assay, coupled with fluorescent probes, to analyse mucin active carbohydrate sulfatase kinetics, cellular location, and inhibition.
Biochemical Society
doi.org
We report plate-based coupled assays to rapidly and quantitatively determine the activity and selectivity of mucin-active carbohydrate sulfatases. This fluorogenic assay further enables inhibitor ide...
Run an MD simulation of any protein in the AlphaFold Protein Structure Database using AF-CALVADOS
Thanks to @sobuelow.bsky.social AF-CALVADOS is now on Colab
colab.research.google.com/github/KULL-...
Kresten Lindorff-Larsen
In our latest chat with #ListerPrize2025 Fellows, Chris Hill @chillzaa.bsky.social at @york.ac.uk shares insights into how enteroviruses use the 3D structure of RNA to hijack host ribosomes.
🔗 lister-institute.org.uk/news/in-conv...
♻️ Make Chris's day: A comment or repost is good for the soul 👇
I'm excited that this collaborative work with Alan @acartmell47.bsky.social is finally out. We have developed some powerful tools to study carbohydrate sulfatases (a tricky class of enzyme!) and shown how they can be used with enzymes from host-associated bacteria.
Now published in Nature Communications:
www.nature.com/articles/s41...
The anomer collapsing advance is something we continue to use today, and we hope others may find it useful.
Furthermore, this library is the largest representation to date of the human N-glycome (3x the next biggest) #glycotime
First paper for PhD student in the Bolam / Lowe labs Natalia Łoś on a the characterisation of a new CBM family that binds (beta) mannan! #glycotime @natalia-los.bsky.social 🥳🥳
link.springer.com/article/10.1...
The Lister Institute of Preventive Medicine
Happy to have this collaborative work with Zach Armstrong now out in Angewandte chemie doi.org/10.1002/anie... .
We use a linked assay, coupled with fluorescent probes, to analyse mucin active carbohydrate sulfatase kinetics, cellular location, and inhibition.
Researchers created N-glycopedia, a reference library of 226 sugar molecules found on proteins, enabling a native glycomics method to precisely identify and measure these sugars, which influence immun...
We report plate-based coupled assays to rapidly and quantitatively determine the activity and selectivity of mucin-active carbohydrate sulfatases. This fluorogenic assay further enables inhibitor ide...
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe.
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
Folddisco enables protein structural motif search in million scale databases.
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
Video
Martin Steinegger 🇺🇦
By deep characterisation of 186 N-glycan standards, we @thencfg.bsky.social have made the most comprehensive targeted LC-MS glycomic assay to date.
Non-reduced native glycan analysis is key.
We hope this enables anyone with QqQ and interest in #glycotime to measure specific N-glycan structures.
link.springer.com
β-mannans are plant structural and storage polysaccharides prevalent in the human diet. Their degradation in the gastrointestinal tract is mediated by the human gut microbiota (HGM) through expression...
We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝
