Science Advances

Supplementary Materials

This PDF file includes:

  • Supplementary Text
  • Supplementary Methods
  • fig. S1. Illustrated descriptions and modeling constraints of all 82 benchmark test cases.
  • fig. S2. Rosetta free energy versus RMSD summaries of SWM modeling runs for 82 complex RNA motifs.
  • fig. S3. Comparison of model accuracy between SWM and fragment assembly of RNA with FARFAR over an 82 motif benchmark.
  • fig. S4. Potential routes to overcome limitations in Rosetta free energy function.
  • fig. S5. Compensatory mutagenesis of the R(1) receptor read out through chemical mapping.
  • fig. S6. Comprehensive single mutant analysis of the tetraloop receptor R(1).
  • fig. S7. Global fold changes between the template viral xrRNA and the Zika xrRNA structure prediction challenge.
  • fig. S8. Other models of RNA-Puzzle 18 (Zika xrRNA).
  • table S1. A comparison of the SWA and SWM methods using the same energy function as the original SWA benchmark set of trans-helix single-stranded loops, and SWM results using the updated Rosetta free energy function (SWM*).
  • table S2. Updates to the Rosetta energy function.
  • table S3. Detailed performance of the stepwise Monte Carlo algorithm on 82 benchmark cases.
  • table S4. Detailed performance of the FARFAR algorithm on 82 benchmark cases.
  • table S5. Measurements of interaction free energy between R(1) mutant tetraloop receptors and GGAA tetraloop.
  • References (35–87)

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Other Supplementary Material for this manuscript includes the following:

  • data file S1. Three-dimensional SWM models canonical 11-nt:GAAA, R(1):GGAA, C7.2:GAAA, and C7.10:GAAA tetraloop/receptors in PDB format.

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