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The R3D-2-MSA (RNA 3D Structure-to-Multiple Sequence Alignment) is a web-based tool for linking 3D structures to multiple RNA sequence alignments.


Molecular modelling; RNA; Sequence analysis


  • Operation: Structure analysis; Multiple sequence alignment
  • Input: PDB/NDB
  • Output: JSON; HTML
  • Software interface: Web user interface
  • Language: -
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: National Institutes of Health (NIH) [GM085328 to N.B.L. and C.L.Z., GM055898 to N.B.L., GM067317 and GM085337 to R.R.G.]; Microsoft Research [UTA08-351 to R.R.G.]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Funding for open access charge: NIH [GM085328 to N.B.L. and C.L.Z.].
  • Contact: ude.usgb _at_ sitnoel
  • Collection: -


Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N "R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server." Nucleic Acids Res. 2015 Jul 1;43(W1):W15-23.
PMID: 26048960
PMCID: PMC4489222

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