| RNA sequence databases contain sequences from hundreds to thousands of homologous molecules. After alignment, these sequences have been successfully mined to reconstruct secondary structures, infer phylogenies, and estimate mutation rates of individual nucleotides and basepairs. Atomic-resolution RNA 3D structures are less numerous, but far more informative than sequence data, as they show, in the ideal case of well-ordered and well-resolved structures, every basepair, base stacking, and base-backbone hydrogen bond.;To function correctly, structured RNA molecules must fold into the correct 3D structure. Since RNA 3D structure is more conserved than RNA primary sequence, detecting structural similarities (and dissimilarities) among RNA 3D structures can produce a wealth of information regarding the functional and evolutionary properties that could not be found by analyzing sequence data alone. The goal of RNA 3D structural alignment is to establish correspondences between the individual nucleotides that are similar in the two 3D structures.;Due to rapid technological developments within the past decade, there has been a dramatic increase in both the size and number of RNA 3D structures that have been crystallized and made available. It is no longer feasible to solely rely on manual comparison of two RNA 3D structures, which can be a labor-intensive and time-consuming process. Consequently, it has become essential to develop tools that are capable of accurately and automatically discovering structural similarities among RNA molecules, which is accomplished through 3D-to-3D alignment. |
