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KIMMDY: a biomolecular reaction emulator

Molecular simulations have become indispensable in biological research. Their accuracy continues to improve, but directly modelling biochemical reactions - central to all life processes - remains computationally challenging. Here, we present a biomolecular reaction emulator that models reactions acr...

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Autori principali: Hartmann, Eric (Autore) , Buhr, Jannik (Autore) , Riedmiller, Kai (Autore) , Ulanov, Evgeni (Autore) , Schüpp, Boris (Autore) , Kiesewetter, Denis (Autore) , Sucerquia, Daniel (Autore) , Aponte-Santamaria, Camilo (Autore) , Gräter, Frauke (Autore)
Natura: Article (Journal)
Lingua:inglese
Pubblicazione: 2026
In: Nature Communications
Year: 2026, Volume: 17, Pages: 1-10
ISSN:2041-1723
DOI:10.1038/s41467-026-71955-2
Accesso online:Verlag, kostenfrei, Volltext: https://doi.org/10.1038/s41467-026-71955-2
Verlag, kostenfrei, Volltext: https://www.nature.com/articles/s41467-026-71955-2
Testo
Note sull'autore:Eric Hartmann, Jannik Buhr, Kai Riedmiller, Evgeni Ulanov, Boris N. Schüpp, Denis Kiesewetter, Daniel Sucerquia, Camilo Aponte-Santamaría & Frauke Gräter
Descrizione
Riassunto:Molecular simulations have become indispensable in biological research. Their accuracy continues to improve, but directly modelling biochemical reactions - central to all life processes - remains computationally challenging. Here, we present a biomolecular reaction emulator that models reactions across conformational ensembles using kinetic Monte Carlo. Our method, KIMMDY, is capable of handling dynamic, large-scale systems with successive, competing reactions, even on the second timescale or slower. It leverages graph neural networks for large-scale prediction of reaction rates, while also being capable of using simpler physics-based or heuristic models. We validate our approach against experimental data and showcase its power and versatility through a series of applications, including radical reactions, nucleophilic substitutions, and photodimerization. Example systems span proteins and DNA. KIMMDY aids the understanding of biochemical reaction cascades in complex systems, helps to re-interpret experimental data, and can inspire future wet-lab experiments.
Descrizione del documento:Online veröffentlicht: 14. April 2026
Gesehen am 18.06.2026
Descrizione fisica:Online Resource
ISSN:2041-1723
DOI:10.1038/s41467-026-71955-2

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