Welcome to ROSIE Rosetta Online Server that Includes Everyone

Overview

RNA Redesign performs fixed backbone design on RNA 3D structures to produce sequences that best stabilize a given 3D conformation. At each position being designed, each nucleotide is tried with set of different chi angles (the dihedral angle between the sugar and base). A summary of the sequences that stablize the submitted 3D structure are displayed in a weblogo to easy see the propensity of a sequence position to specific nucleotides. All designs are available to download and summerized in a table that can be sorted by Rosetta energy.

Tips

1. Input and output PDB models have residues marked rA, rC, rG, and rU, due to historical reasons. If you supply a "standard" PDB file as a native reference model, it will be converted to this format automatically. PDBs with non-standard nucleotides (e.g,. dihydroxyuridine) will not be handled properly. If you run into issues, try the conversion yourself with this python script.
2. If there are only a few residues of interest, specify them in the optional text box. This will greatly speed up the run time.

Inputs

1. PDB file: The pdb file of standard PDB format.
2. Residues to design [Optional]: by default all residues will be designed, if there is only a section of the structure needs to be designed its possible to specify it. . Format: ChainName:FirstResidue-LastResidue, Example: A:90-100,B:2-4,C:10. In this case residues 90 to 100 on chain A, residues 2 to 4 on chain B and residue 10 on chain C will be designed while the rest will retain their native nucleotide.
3. Number of requested designs: the number of designs to be generated, default (100), not necessarily unique from each other.

Interpreting Results

1. Displays a web logo to see the propensity of a nucleotide to a location in the 3D structure.
   
2. The server shows pictures of the best-scoring sequences. Click on the [Model-N] link to download the PDB file
3. Finally you'll also get a score break down of all the models, which helps explain the energetics that go into Rosetta all-atom refinement for RNA

   score                                            Final total score
   fa_atr                                           Lennard-jones attractive between atoms in different residues
   fa_rep                                           Lennard-jones repulsive between atoms in different residues
   fa_intra_rep                                     Lennard-jones repulsive between atoms in the same residue
   fa_elec_rna_phos_phos                            Simple electrostatic repulsion term between phosphates
   lk_nonpolar                                      Lazaridis-karplus solvation energy, over nonpolar atoms
   ch_bond                                          Carbon hydrogen bonds
   rna_torsion                                      RNA torsional potential.
   rna_sugar_close                                  Term that ensures that ribose rings stay closed during refinement.
   hbond_sr_bb_sc                                   Backbone-sidechain hbonds close in primary sequence
   hbond_lr_bb_sc                                   Backbone-sidechain hbonds distant in primary sequence
   hbond_sc                                         Sidechain-sidechain hydrogen bond energy
   geom_sol                                         Geometric Solvation energy for polar atoms
   

We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.

RNA modeling tools developed by the Das lab at Stanford