Developing bioinformatics software in Steinegger lab. at Seoul National Univ.
Jaebeom Kim
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Structural motif search across the protein universe with Folddisco - @martinsteinegger.bsky.social go.nature.com/4g8lCb0
Metabuli now features three layers of mismatch tolerance: synonymous DNA mutations, conservative amino acid substitutions, and substitutions in joker positions. Additionally, we've introduced E-value-based filtering to discard noisy matches.
Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv.
Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen)
github.com/bluenote-157...
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45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript:
• 12 high-confidence folds in AFESM
• 33 by ColabFold-repredicting 2.3M low-quality domains
We show AFDB captures most domains already and ESMfold struggles with novelty
🌏 afesm.foldseek.com
📄 biorxiv.org/content/10.1...
Folddisco enables protein structural motif search in million scale databases.
Metabuli App v1.2 makes Metabuli easier to use on desktop! Run taxonomic profiling, curate databases, and visualize results locally. 🚀 No command line, no server setup, no internet required. Download the app from github.com/steineggerla...
Our pre-built RefSeq, HGRM2, and HROM databases have Kraken2/Braken counterparts. You can use these Braken databases directly alongside Metabuli to estimate species abundance.
Please check the docs: jaebeom-kim.github.io/metabuli-doc...
Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.
As an organizer, it was great to see such a large student participation! As a metagenomics researcher, learning about reference microbiome/virome was very helpful to my studies.
Nature Biotechnology
Does your designed active site already exist in nature? Is an uncharacterized protein hiding a catalytic site or a pocket? Folddisco answers both, searching millions of structures for a 3D motif in seconds.
@natbiotech.nature.com 🧬
📄 www.nature.com/articles/s41...
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Jaebeom Kim
Foldseek clustered 820M AlphaFold DB + ESMatlas structures
Updated the app to use Metabuli v1.2.0, the version used in "Sensitive and scalable metagenomic classification using spaced metamers, reduced alphabets, and syncmers"
github.com
Sensitive and specific metagenomic classification via joint analysis of amino acid and DNA
