●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

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.

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

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

• 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]