Full stack developer who occasionally wears a lab coat. Currently a machine learning researcher at Manifold Bio.
Ernst Schmid
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Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster:
www.biorxiv.org/content/10.1...
github.com/TravisWheele...
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...
🧵1/7👇
My latest work! We found that the autoproteolytic GAIN domain which mediates force responsive signaling in adhesion GPCRs is not unique to eukaryotes. The microbial counterparts anchor diverse adhesion, enzymatic, and toxin domains to the cell surface, enabling release by likely mechanical stimuli.
Microbial GAIN domains undergo autoproteolysis and enable release of diverse cell surface associated proteins https://www.biorxiv.org/content/10.64898/2026.05.12.724683v1
Now published in NSMB!
Paper: doi.org/10.1038/s415...
Full PDF: rdcu.be/fhBtI
Overview of additions since the preprint👇 (1/5)
Ph.D. finished! So many people to thank (pictured) but especially B. subtilis (& S. aureus & B. anthracis) (not pictured)
