While most of these applications focus on prediction, many have options which will also allow design.

  • Ab initio modeling: Predict 3-dimensional structures of proteins from their amino acid sequences.
  • Backrub: Create backbone ensembles using small, local backbone changes.
  • Comparative modeling: Build structural models of proteins using one or more known structures as templates for modeling.
  • Floppy tail: Predict structures of long, flexible N-terminal or C-terminal regions.
  • Fold-and-dock: Predict 3-dimensional structures of symmetric homooligomers.
  • Molecular replacement protocols: Use Rosetta to build models for use in X-ray crystallography molecular replacement.
  • Relax: "Locally" optimize structures, including assigning sidechain positions.
  • RNA : see below for apps, including FARFAR & ERRASER (crystallographic refinement).
  • RosettaNMR with Paramagnetic Restraints: Structure prediction in RosettaNMR using backbone chemical shifts and paramagnetic restraints derived from metal ion tags.

Loop Modeling

RNA and RNA/protein

  • RNA structure prediction: Predict 3-dimensional structures of RNA from their nucleotide sequence. Read this first.
    • RNA tools: Tools useful for RNA and RNA/proteinm including general PDB editing, cluster submission, job setup.
    • RNA threading: Thread a new nucleotide sequence on an existing RNA structure.
    • 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. See also Stepwise monte carlo.
  • Stepwise monte carlo: Generate 3D models of protein, RNA, and protein/RNA loops, motifs, and interfaces. Stochastic version of stepwise assembly.
  • RNA assembly with experimental constraints: Predict 3-dimensional structures of large RNAs with the help of experimental constraints. Note – largely deprecated by newer pipeline (documentation coming soon).
  • ERRASER: Refine an RNA structure given electron density constraints.
  • Sample around nucleobase: Visualizing energy functions by scanning probe molecules around a nucleobase.
  • RECCES: RNA free energy calculation with comprehensive sampling.
  • RNA pharmacophore: Extract and cluster the key features present in RNA (rings, hbond donors & acceptors) from the structure of a protein-RNA complex.

Antibody Modeling

TCR Modeling

See Also