RNA Structure Refinement using the ERRASER-Phenix pipeline
By Fang-Chieh Chou, Nathaniel Echols, T. C. Terwilliger, Rhiju Das. 2013
29 citations recorded by the source corpus.
The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by Rfree). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).
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Citations in the corpus
- Structural Insights into the Mammalian Late-Stage Initiation Complexes (2020, methodology): “ERRASER (Chou et al., 2016) Visual Molecular Dynamics (Humphrey et al., 1996) https://www.ks.uiuc.edu/Research/vmd/ Scalable Molecular Dynamics 2 (Phillips et al., 2005) http://www.phenix-online.org/”
- Using Rosetta for RNA homology modeling (2019, unknown): “For this test, we select the B. subtilis guanine riboswitch (PDB ID 1Y27) (Serganov et al., 2004) and we run the structure through the ERRASER-Phenix pipeline.”