RNADyn: A Benchmark for Generating and Understanding RNA Dynamics

Abstract:Ribonucleic acid (RNA) functions through conformational changes that are not fully captured by static structures. However, large-scale standardized RNA dynamics data remain limited, and existing approaches typically treat trajectory generation and dynamics understanding as separate objectives. Here, we introduce RNADynBench, a standardized RNA molecular dynamics (MD) benchmark with 2585 quality-controlled 100-ns all-atom trajectories and leakage-controlled splits. Building on RNADynBench, we develop RNADynNet, a unified model for RNA dynamics learning that uses a shared backbone for both trajectory generation and dynamics fingerprint extraction from a single conformer. It combines coordinate denoising, single-frame-to-trajectory alignment, and physical grounding to connect all-atom trajectory generation with dynamics representation learning. Physical grounding improves both generated dynamics and the physical information recoverable from these fingerprints. Across both test sets, including the high-flexibility challenge set, the generated trajectories achieve RMSF correlations of 0.875 and 0.766, while single-conformer predictions show comparable agreement with MD-derived dynamics. RNADynBench and RNADynNet together establish a benchmark and unified modeling framework for generating and understanding RNA dynamics.

Machine Learning (cs.LG); Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

arXiv:2610.03712 [cs.LG]

(or arXiv:2610.03712v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2610.03712 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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