Global health challenges demand a deep understanding of cellular machinery at a molecular level, with RNA molecules playing a pivotal role. In the last years, the field of epitranscriptomics which consists of functional chemical modifications in RNA, has shown rapid growth [1]. RNA modifications are linked to various diseases, such as cancer or inflammatory and autoimmune diseases. Over a hundred nucleotide modifications have been documented, encompassing 5-methylcytosine (m⁵C) and N6-methyladenosine (m⁶A) [2,3]. Among these, the latter stands out as the most prevalent modification, influencing all RNA types across diverse organisms. Within mammalian cells, m⁶A modulates gene expression, consequently influencing cellular functions such as stress response and stem cell differentiation. Epitranscriptomic modifications play a crucial role in the innate immune system's detection of non-self RNA. This critical insight enabled the successful engineering of mRNA vaccine tolerance and positioned RNA modifications and the enzymes responsible for them as compelling therapeutic targets. Therefore RNA modifications appear critical both for using RNA as a drug, and as a drug-target. Despite their crucial roles, our understanding of the effect of these modifications on RNA structure, dynamics, and function is still limited [4]. Several enzymes such as RNA methyltransferases that regulate gene expression and metabolism  [5-7], ADAR , an enzyme converting adenosine to inosine [8], or terminal uridylyltransferases—that catalyze the 3’ end untemplated addition of uridines [9,10] are pivotal.  Targeting these RNA-modifying enzymes is a promising strategy for drug design, with a need to find small molecules specific to these new targets. The success of such development is intimately dependent on the avaibility of the structures and on our understanding of the molecular mechanisms that govern them, in particular the underlying chemical reaction and the inhibition at molecular level. Moreover, better understanding RNA modifications will improve the efficacy and safety of mRNA vaccines [11]. To do so, the combination of molecular modelling [12], bioinformatics [13] and experiments is essential [14,15]. 

In parallel, RNA modifications are also used to probe RNA structures via a variety of chemical probing experiments [16]. These techniques have been developed to overcome the limitations in obtaining high-resolution 3D structures for RNA [17]. Chemical probing has extensively been used to constrain RNA 2D structure prediction algorithms, which drastically improve predictions [18,19]. Chemical probes can interrogate the Hoogsteen or Watson-Crick face of the base, as well as the sugar–phosphate backbone via different chemical modifications. Some examples are provided by dimethyl sulfate which methylates the nucleobases at different positions or SHAPE reagents reacting with the ribose 2’-OH of flexible nucleotides [16]. Despite the improvement in the prediction of the 2D structures, several questions remain open since several reactivities remain unexplained and the difficulties to translate these pieces of the information in the prediction at 3D level [20-23]. Therefore, there is the need to combine different modelling and bioinformatics approaches in relation to various sets of experimental data. Moreover, the study of functional RNA modifications presents challenges for experimental methods: on the one hand, only a few high-resolution structures with modified nucleotides are available; on the other hand, chemical probing techniques may struggle to detect these modifications.