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Many RNA molecules are posttranscriptionally modified. This means that specific positions in the RNA chain are chemically changed by enzymes, mostly adding extra chemical groups. RNA modifications are most abundant in tRNA, where about 20% of the residues are modified. They stabilize the tRNA tertiary structure, increase the accuracy of recognition by proteins from the [...]

Base pairs are the most important interaction found in folded RNA. Formed by hydrogen bonding, both classical Watson-Crick pairs (A-U, G-C) and wobble base pairs (G-U) can be found frequently – the bases then are oriented in the same way as in DNA. These are termed canonical base pairs (70%). Less frequently (30%), the nucleotide [...]

A very useful model of RNA structure is considering only the Watson-Crick base pairs (G+C, A+U, and the Wobble base pair G+U). These are also called canonical base pairs and define the secondary structure or 2D structure of an RNA molecule. In the secondary structure, characteristic elements can be identified: helical stems, loops, bulges, internal [...]

RNABuilder is a program for RNA 3D structure modeling. It allows the user to specify a set of constraints for base pairing and stacking, distance restraints, rigidifying portions of the molecule, and many more. In practice, these can be combined to thread a RNA chain to one or more structural templates, and relax the structure [...]