FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

By Michael Sarver, Craig L. Zirbel, Jesse Stombaugh, Ali Mokdad, Neocles Leontis. Journal of Mathematical Biology, 2007

295 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b10a4c1873995aefd5ef7703da30e1d4d072d36f

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Citations in the corpus

Using Rosetta for RNA homology modeling (2019, background): “Packages like RMdetect and FR3D can discover some simple RNA motifs automatically, including kink turns (Cruz & Westhof, 2011; Sarver, Zirbel, Stombaugh, Mokdad, & Leontis, 2008), although we typically still recommend inspecting sequence-conserved regions of the predicted secondary structure of…”
DSSR: an integrated software tool for dissecting the spatial structure of RNA (2015, background): “If the isolated pairs and pseudoknotted stem are not taken into account, the structure appears to form a [6,1,8,3] four-way junction loop as originally reported (48).”
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, unknown): “We are therefore hopeful about further development of RNA structural bioinformatics approaches such as Rmdetect (Cruz and Westhof 2011) and FR3D (Sarver et al. 2008).”
New prediction categories in CASP15 (2023, methodology): “This is done using 2D structure annotators such as RNAView, 21 MC-Annotate, 22 ClaRNA 23 or FR3D, 24 which provide base pairs and their classification.”
Current approaches in SELEX: An update to aptamer selection technology. (2015, methodology): “, 2010), FR3D (Sarver et al., 2008), R3D Align (Rahrig et al.”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, background): “2 tetraloop receptor The FR3D program (25) can search motifs using both geometric (RMSD-like) and/or symbolic (relation-based) criteria.”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, unknown): “To classify contacts by their biochemical interaction type, we used crystal structure annotations from FR3D (Petrov et al., 2011; Sarver et al., 2008) which were downloaded from RNA3DHub (http://rna.bgsu.edu/rna3dhub/).”
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008, background): “Both S1 and S2 motifs can occur within somewhat variable contexts, including even non-continuous strands (Sarver et al. 2007), but both types are usually flanked by regular A-form double helix on both sides.”
Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts (2014, background): “27); (6) HIV-1 TAR apical loop (PDB: 1ANR28); (7) tRNAi ASL (PDB: 1SZY29); (8) conserved SRP internal loop (PDB: 1LNT19, PDB: 28SR3, PDB: 28SP3); (9) R2 retrotransposon 4x4 loop (PDB: 2L8F30); (10) hepatitis C virus IRES IIa (PDB: 2PN4; ref.”
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes (2014, methodology): “The ModeRNA stacking detection algorithm uses a precise version of this criterion; however, the current versions of MC-Annotate (5) and FR3D (7) appear to use a more relaxed criteria, as we found that they report stacking for some other residue pairs (e.”