KIMMDY: our biomolecular reaction emulator - Now on bioRxiv!

We proudly present our new and updated biomolecular reaction emulator KIMMDY (Kinetic Monte Carlo / Molecular Dynamics), now on bioRxiv! Do you want to emulate large reactive systems, up to the second timescale? Read more below!

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. 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!

Read more about our KIMMDY on bioRxiv or try it out yourself here!