Using Rosetta for RNA homology modeling
By Andrew M. Watkins, R. Rangan, Rhiju Das. 2019
16 citations recorded by the source corpus.
The three-dimensional structures of RNA molecules provide rich and often critical information for understanding their functions, including how they recognize small molecule and protein partners. Computational modeling of RNA 3D structure is becoming increasingly accurate, particularly with the availability of growing numbers of template structures already solved experimentally and the development of sequence alignment and 3D modeling tools to take advantage of this database. For several recent “RNA puzzle” blind modeling challenges, we have successfully identified useful template structures and achieved accurate structure predictions through homology modeling tools developed in the Rosetta software suite. We describe our semi-automated methodology here and walk through two illustrative examples: an adenine riboswitch aptamer, modeled from a template guanine riboswitch structure, and a SAM I/IV riboswitch aptamer, modeled from a template SAM I riboswitch structure.
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Citations in the corpus
- Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “27-dev60818-134-g04678680f9c).(40) For the CPEB3 ribozymes (R1107 and R1108), we generated template-based structures using the HDV ribozyme structure (PDB ID: 3NKB).”
- FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “…nucleotides 72–91, and the three final (PDB: 2YGH) and largely followed our previously described procedure for homology modeling of complex RNA folds (Watkins et al., 2019), but used the FARFAR2 protocol instead, i.e., base-pair step sampling for helices, the updated fragment library, and the…”
- Recent advances in RNA structurome (2022, methodology): “, 2011), RNAbuilder (Flores and Altman, 2010), and Rosetta (Watkins et al., 2019), have been developed to build RNA homology models.”