Mathematics and Statistics Faculty Publications


Automated Classification of RNA 3D Motifs and the RNA 3D Motif Atlas

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Modular RNA 3D motifs are the building blocks of complex RNA molecules and RNA-based nanomachines, such as the ribosome and the spliceosome. We have created the RNA 3D Motif Atlas, the first comprehensive and regularly updated catalog of RNA hairpin and internal loop motif instances based on a nonredundant set of PDB structures ( The Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. The potential applications of the Motif Atlas include predicting RNA 3D structures from sequence, designing new RNA nanostructures, and developing new methods for finding RNA 3D motifs in genomic sequences., The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (, which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.

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