Comparison of RNA 3D Structures




Run Rclick




Our server Rclick is capable of superimposing the RNA 3D structures by using the CLICK algorithm of clique matching and 3D least squares fitting. Here, the server first looks for cliques of points formed in the that are structurally similar in the pair of RNA structures to be aligned. Using these local alignments, a one-to-one equivalence is charted between residues of the two structures being compared. A least square fit then superimposes the two structures.

Our server Rclick has been benchmarked and compared to other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were statistically significantly better in terms of structure overlap. The method also recognizes conformational changes that may have occurred in structural regions in one structure with respect to the other. For this purpose, the server produces complementary alignments between the regions that have undergone a conformational change. To the best of our knowledge this is the first RNA structure comparison server that recognizes conformational changes in the RNA structures being compared. The following link ( shows Rclick alignments of two RNA aptamer structures, PDB codes 1OOA:D and 2JWV:A. With conformational change, Rclick shows two alignments between 1OOA:D and 2JWV:A, while other web servers and methods such as ARTS, SARA, SETTER, RASS, and R3DAlign produce only one alignment.

The user is required to upload the pair of RNA structures to be aligned in PDB format, or to specify the 4 letter codes for structures that have already been deposited in the PDB. The resulting 3D superimposition of the two structures can be viewed using the embedded JSMol viewer. Below the 3D rendering of the alignment are details of the alignment such as structure overlap, RMSD, sequence identity, topology score, and fragment score. Help pages inform the users about how these different measures are computed.

Various examples showcase the utility of our web server for comparison of large ribosomal subunits, RNA-protein complexes, RNA-ligand structures. These examples show the utilities of our web server that not only produce accurate alignments of RNA structures but also aid in the general area of prediction of RNA-protein and RNA-ligand interactions.