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RNA-align is an algorithm for comparing 3D structures of RNA molecules. Starting from two RNA structures, RNA-align seeks optimal nucleotide-to-nucleotide alignments based on a heuristic dynamic programming iteration process, assisted by distance-based secondary structure assignments. The structural similarity of the selected alignment is assessed by a renormalized TM-score on the statistics of RNA structures in the PDB, where TM-score_RNA has values in (0,1] with 1 indicating a perfect structure match and a score ≥0.45 corresponding to a structural similarity of the RNA pairs in the same Rfam family. RNA-align can also be used to compare double-stranded DNA structures.

News: RNA-align was extended to US-align which enables monomeric and complex structural alignments between proteins, RNAs and DNAs.

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RNA-align on-line (RNA example output; DNA example output)

Only first chain of an RNA structure or the first two chains of a DNA structure in a PDB file is used for alignment.
Input Structure 1 in PDB or PDBx/mmCIF format (mandatory):
Copy and paste your structure here. Sample RNA input Sample DNA input

Or upload the stucture file:




Input Structure 2 in PDB or PDBx/mmCIF format (mandatory):
Copy and paste your structure here. Sample RNA input Sample DNA input

Or upload the stucture file:


Advanced options

• Whether to assume residue index correspondence between the two structures?
  Sequence independent structure alignment (default).
  Sequence dependent superposition (assume correspondence between a pair of residues with the same residue index in the two structures).
  
• Which backbone atom is used to represent a residue?
  C3' (recommended). C4' C5' O5' O3' P

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RNA-align download

• Download the new TM-align package that unifies protein and RNA/DNA structure alignmnet.
• Download RNA-align standalone program and benchmark datasets.

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References:

• Sha Gong, Chengxin Zhang, Yang Zhang. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-score_RNA. (2019) Bioinformatics, 35: 4459-4461. [PDF] [Supplement]