Author

Vít Škrhák

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Open access Aug 2026

EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology

EmmaEmb is introduced, a quantitative, model-agnostic framework for geometric correction, direct analysis, and comparison of embedding spaces that encompasses local and global analysis methods to quantify data distribution within an embedding space and enable comparisons of representations across spaces in relation to...

Pia Francesca Rissom, Vít Škrhák, Paulo Yanez Sarmiento et al. · Patterns · 0 citations

Open access Jul 2026

Decoding the allosteric grammar of protein kinases: A dual‐stream framework integrating protein language models and energy landscape frustration analysis

This study reveals how the organization of the protein energy landscape shapes universal "allosteric grammar" and algorithmic detectability of regulatory binding sites and proposes that allosteric sites are encoded in persistent neutrally frustrated regions optimized for context‐dependent regulatory modulation.

Will Gatlin, Max Ludwick, L. Turano et al. · Protein Science · 1 citation