Author

Carlos F. Lopez

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Open access Sep 2026

Folding-Driven Control of the Functional PP1 Complex via Multiscale Modeling

Understanding how conformational dynamics regulate protein complex assembly remains a central challenge in molecular systems biology. Here, we develop a multiscale modeling framework that integrates all-atom molecular dynamics (MD) simulations with rule-based kinetic modeling to investigate formation of the PP1–GADD34–...

Federico Fontana, Bryan A. Bogin, Michael W. Irvin et al. · bioRxiv · 0 citations

Open access Aug 2026

Deep learning of dynamic signatures resolves mechanistic ambiguity in complex signaling networks

An AI-driven framework treating model dynamics as learnable signatures is introduced, using deep learning autoencoders to embed the dynamic signatures of thousands of competing models into a low-dimensional latent space and provides a rigorous, full-state alternative to scalar metrics.

Mustafa Ozen, Chaitra Agrahar, Francesca Zappa et al. · bioRxiv · 0 citations