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Using Rosetta for RNA homology modeling.

Authors
  • Watkins, Andrew M1
  • Rangan, Ramya2
  • Das, Rhiju3
  • 1 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States. , (United States)
  • 2 Biophysics Program, Stanford University, Stanford, CA, United States. , (United States)
  • 3 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States; Biophysics Program, Stanford University, Stanford, CA, United States. Electronic address: [email protected] , (United States)
Type
Published Article
Journal
Methods in enzymology
Publication Date
Jan 01, 2019
Volume
623
Pages
177–207
Identifiers
DOI: 10.1016/bs.mie.2019.05.026
PMID: 31239046
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

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. © 2019 Elsevier Inc. All rights reserved.

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