Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Summary Although chemically close to DNA, RNA can adopt a wide range of structures from regular helices to complex globular conformations, showing a complexity similar to that of proteins. The determination of the structure of RNA molecules, crucial for functional understanding, is severely handicapped by their size and flexibility, which makes the systematic use of experimental approaches difficult. Simulation techniques are also suffering from very severe problems related to the accuracy of the methods and their ability to sample a large and complex conformational landscape. Here, we systematically review recent approaches created to reduce the shortcoming of the current generation of simulation methods—from highly accurate models able to deal with small systems to coarse-grained approaches that are less accurate but applicable to dealing with large models.