Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density
- 14 October 2022
- book chapter
- Published by Springer Nature
- Vol. 2568, 193-211
Abstract
RNA three-dimensional structures provide rich and vital information for understanding their functions. Recent advances in cryogenic electron microscopy (cryo-EM) allow structure determination of RNAs and ribonucleoprotein (RNP) complexes. However, limited global and local resolutions of RNA cryo-EM maps pose great challenges in tracing RNA coordinates. The Rosetta-based “auto-DRRAFTER” method builds RNA models into moderate-resolution RNA cryo-EM density as part of the Ribosolve pipeline. Here, we describe a step-by-step protocol for auto-DRRAFTER using a glycine riboswitch from Fusobacterium nucleatum as an example. Successful implementation of this protocol allows automated RNA modeling into RNA cryo-EM density, accelerating our understanding of RNA structure–function relationships. Input and output files are being made available at https://github.com/auto-DRRAFTER/springer-chapter. Key words RNA structure Cryo-EM Auto-DRRAFTER Rosetta computational modelingKeywords
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