When Does Molecular Dynamics Improve RNA Models? Insights from CASP15 and Practical Guidelines

This dataset accompanies the manuscript “When Does Molecular Dynamics Improve RNA Models? Insights from CASP15 and Practical Guidelines.” It contains the full set of results from systematic all-atom molecular dynamics simulations performed on RNA models from the 15th Critical Assessment of Structure Prediction (CASP15) experiment. The dataset provides a benchmark of MD refinement applied to 61 RNA structural models across nine CASP15 targets. Each model, plus the corresponding experimental structure, was subjected to 300 nanosecond simulations using the AMBER ff99bsc0χOL3 force field. The archive includes structural snapshots in PDB format saved every 10 ns for all 61 trajectories. It also contains a single tab-separated file with time-series data for root-mean-square deviation (RMSD) and interaction network fidelity (INF) metrics, allowing for direct analysis of model quality over time. This dataset is a valuable resource for benchmarking RNA force fields, developing new refinement strategies, and training machine learning models for structure validation and scoring. The initial, pre-simulation structures (i.e., the models as submitted to CASP15) are not part of this deposit. They can be downloaded directly from the official CASP website: https://predictioncenter.org/casp15/