JAR3D scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.
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JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Roll J, Zirbel CL, Sweeney B, Petrov AI, Leontis N.
Nucleic Acids Res. 2016 May 27. pii: gkw453
Identifying novel sequence variants of RNA 3D motifs,
Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis.
Nucleic Acids Res. 2015 Sep 3;43(15):7504-20. doi: 10.1093/nar/gkv651