Case study: MARS-RNA

1AUD case study (MARS‑RNA) This dataset contains input and derived files used in the MARS‑RNA case study on the 1AUD RNA structure. It is intended to illustrate the full pipeline from molecular dynamics (MD) simulation to feature extraction and correlation analysis for RNA conformational modeling. Input files: 1AUD_shape.shape Experimental SHAPE reactivity profile for the 1AUD RNA, used as structural probing input for MARS‑RNA. index.ndx GROMACS index file defining atom/residue groups (e.g., nucleotide selections) used for trajectory analysis. md-1AUD.xtc Compressed GROMACS trajectory of the 1AUD RNA MD simulation, providing the time-resolved conformational ensemble. md-2.tpr GROMACS portable run input file (topology, parameters, starting coordinates) corresponding to the MD run used in this case study. min_RNA.gro GROMACS coordinate file containing the minimized RNA structure that serves as the starting conformation for the MD simulation. Output files: results_corr_fit/1AUD_features.csv Raw feature matrix extracted from the MD trajectory and structural annotations. results_corr_fit/1AUD_correlations.csv Correlation results between MARS‑RNA model outputs and experimental profile for the 1AUD system. results_corr_fit/1AUD_features_preprocessed.csv Preprocessed feature matrix (e.g., filtered, normalized, or transformed) ready for model training or evaluation. results_corr_fit/pdbs.json Concatenated DSSR JSON output for all frames in pdbs.pdb. results_corr_fit/pdbs.pdb Representative PDB structures derived from the MD trajectory and linked to the feature/correlation files.