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These applications are specifically designed to work with RNA or RNA-protein complexes. For more information on working with RNA in Rosetta, see the Working with RNA page.

RNA Structure Prediction

  • 3D RNA structure prediction: Predict 3-dimensional structures of RNA from their nucleotide sequence. Read this first.
  • RiboKit What experiments & analysis to do to obtain 3D RNA models.
  • RNA motif prediction: Model RNA motifs with fragment assembly of RNA with full atom refinement (FARFAR).
  • RNA stepwise loop enumeration: Build RNA loops using deterministic stepwise assembly.
  • Stepwise monte carlo: Stochastic version of stepwise assembly used to generate 3D models of proteins, RNA, and protein/RNA loops, motifs, and interfaces. This application is not exclusively for RNA but is compatible.
  • RNA assembly with experimental constraints - Predict 3-dimensional structures of large RNAs with the help of experimental constraints. Note – largely deprecated by newer pipeline (described in this paper and demo).
  • CS Rosetta RNA: Refines and scores an RNA structure using NMR chemical shift data.
  • auto-DRRAFTER: Builds RNA coordinates into cryo-EM maps (currently for maps that do not contain proteins).
  • DRRAFTER: Builds RNA coordinates into cryo-EM maps of RNA-protein assemblies.
  • Structure prediction of RNA-protein complexes: Predict 3D structures of RNA-protein complexes.

RNA Design

  • RNA design: Optimize RNA sequence for fixed backbones.

RNA Analysis

  • RECCES: RNA free energy calculation with comprehensive sampling.
  • rnp ddg: Calculate relative binding affinities for RNA-protein complexes with the Rosetta-Vienna ΔΔG method.

RNA Utilities

  • RNA tools: A collection of tools for PDB editing, cluster submission, "silent file" processing, and setting up rna_denovo and ERRASER jobs.
  • ERRASER: Refine an RNA structure given electron density constraints.
  • RNA pharmacophore: Extract and cluster the key features present in RNA (rings, hbond donors & acceptors) from the structure of a protein-RNA complex.
  • RNA threading - Thread a new nucleotide sequence on an existing RNA structure.
  • Sample around nucleobase: Generates tables of interaction energies between an adenosine nucleobase and a user-specified probe.
  • RNA score: a simple scoring application with hooks into preferred RNA workflows. Not superior to score_jd2 intrinsically, but usually more convenient.
  • RNA chemical modifications: discussion of how to model RNAs with chemically modified nucleotides.

See Also