R3D Align

Decomposes 3D structure into sets of local nucleotide neighbourhoods, which typically overlap in the sense that each nucleotide is included in more than one set. R3D Align is a web server that for locally optimized, nucleotide to nucleotide pairwise alignments of RNA 3D structures. It also provides additional features: all RNA chains present in the protein data bank (PDB) file are dynamically loaded into the input page to allow the user to specify chains and nucleotide ranges to align.