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

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.

See Also