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.
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Cite this article
APA 7
Huang, Y., Bastian, L., Cao, H., Vollmers, L., & Birdal, T. (2026). RNADyn: A Benchmark for Generating and Understanding RNA Dynamics. https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics
MLA 9
Huang, Yiming, et al. "RNADyn: A Benchmark for Generating and Understanding RNA Dynamics." https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics.
Chicago (author–date)
Huang, Yiming, Lennart Bastian, Hanqun Cao, Luis Vollmers, and Tolga Birdal. 2026. "RNADyn: A Benchmark for Generating and Understanding RNA Dynamics." https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics.
Harvard
Huang, Y., Bastian, L., Cao, H., Vollmers, L. and Birdal, T. (2026) 'RNADyn: A Benchmark for Generating and Understanding RNA Dynamics', Available at: https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics.
Vancouver
Huang Y, Bastian L, Cao H, Vollmers L, Birdal T. RNADyn: A Benchmark for Generating and Understanding RNA Dynamics. https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics
IEEE
Y. Huang, L. Bastian, H. Cao, L. Vollmers, and T. Birdal, "RNADyn: A Benchmark for Generating and Understanding RNA Dynamics," https://omanscience.com/en/articles/rnadyn-a-benchmark-for-generating-and-understanding-rna-dynamics.