We investigated the capability of internal normal modes to reproduce RNA dynamics and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified rep- resentation of RNA structure and its potential energy. In this study, we considered three main data sets to investigate different aspects : i) one based on single-stranded RNA molecules for which all-atom MD simulations were computed; ii) one based on the available structures belonged to a specific Rfam family; iii) one based on the transition from unbound to bound RNA. In each folder modes.dat: results obtained by iNMA (frequency and normal modes) das1.dat: conversion from internal to cartesian normal modes Each file name_enm.pdb refers to a PDB structure with a CG representation (RNA three-bead model). Dataset 1: d1.zip For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis, the results obtained by iNMA for different values of distance cut-off Rc and some scripts. Matlab and python scripts: analysis_pca.py: to extract the different principal components analysis_PCA.m: to compute overlap and cumative overlap in each folder analysis_complete_new.m: to summarize the results Dataset 2: d2.zip For this dataset, we provide the structure ensemble for Rfam family and the results obtained by iNMA for different values of distance cut-off Rc and some scripts. PDB files: allensemble.pdb: ensemble of PDB structures for a given Rfam family allensemble_enm.pdb: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model) allensemble_enm_new.pdb: ensemble of PDB structures for a given Rfam family with the same number of atoms for each model converted to CG representation (RNA three-bead model) model.pdb: reference PDB structure model_enm.pdb: reference PDB structure converted to CG representation (RNA three-bead model) Matlab script: pca_xray_anal.m: PCA analysis, overlap, cumulative overlap, rmsip and plots Dataset 3: d3.zip PDB structure: bound.pdb: bound structure unbound.pdb: unbound structure diff.dat: difference between bound and unbound structure after superimposition RMSDn with n a number: the first column represents \(\sqrt{\beta/2}\) Matlab script: rmsd_anal.m: analysis best mode based on RMSD Application to the CrPV-IRES: IRES.zip PDB structures: IRES_cg.pdb: Coarse-grain structure based on the PDB ID 5IT9 b_end001_01_70.pdb, b_end001_01_80.pdb, b_end001_01_90.pdb: Example of modified structures using the first lowest modes and different amplitudes \(\beta\) b_end002_03_50.pdb, b_end002_03_60.pdb, b_end002_03_70.pdb: Example of modified structures using the third lowest modes and different amplitudes \(\beta\)