Comprehensive examination of RNA structure and function can yield insights Impossible to giean from analysis of individual molecules. To aid understanding of the large and rapidly growing corpus of RNA structural data, we propose to create a structural classification of RNA (scaR). This database will organize features at four levels of complexity: three-dimensional motifs, tertiary interactions, structural domains, and whole molecules. Each of these may have multiple means of organization; for example, both by loop size and by base stacking. To initially define significant recurrent features, the classification will begin with manual inspection of all RNA structures. As the project progresses, observed characteristics will be formalized into algorithms that will be applied to perform rapid, reproducible, and accurate analysis and classification of RNA structures. The structural features will be mapped into a functional classification, and the associations between the two will be used to study general relationships between aspects of RNA structure and their function. To explore the evolutionary basis of RNA structure and the dependence of structure upon sequence, detailed links will be forged between classified RNAs of known structure and their evolutionarily related families. This classification will immediately elucidate the prevalence and variability of features in RNA structure. In addition, it is expected to have applications in RNA molecular modeling, molecular design and engineering, and RNA ligand and drug design. It will greatly enhance our understanding of RNA structure-function relations, the correlation between RNA structure and physical and biological properties, and evolutionary effects on RNA structure. The database will also provide a convenient and logical means for experts and neophytes alike to access and interpret the growing wealth of RNA sequence and structural data.
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