Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling

摘要: In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in linear sequence. While there numerous methods for computational prediction protein 3D from sequence, have been however very few such RNA. This chapter discusses template-based template-free approaches macromolecular prediction, with special emphasis comparison between already tried-and-tested modeling recently developed “protein-like” As examples, we briefly review our tools including ModeRNA (template-based or comparative/homology modeling) SimRNA (template-free de novo modeling). requires, as an input, atomic coordinates a template molecule user-specified sequence alignment target be modeled template. It can model posttranscriptional modifications, functionally important feature analogous posttranslational modifications proteins. structures RNAs essentially any length, provided that starting is known. fold alone. based coarse-grained representation polynucleotide chains (only three atoms per nucleotide) uses Monte Carlo sampling scheme generate moves space, statistical potential estimate free energy. The current implementation simulated annealing able find native-like conformations <100 nt multiple runs required long sequences.