Rosetta 3.1 Release Manual

RNA Structure Modeling

The RNA structure modeling algorithm in Rosetta is based on the assembly of short fragments from existing RNA crystal structures whose sequences match subsequences of the target RNA. The Fragment Assembly of RNA (FARNA) algorithm is a Monte Carlo process, guided by a low-resolution knowledge-based energy function. The models can then be further refined in an all-atom potential to yield more realistic structures with cleaner hydrogen bonds and fewer clashes; the resulting energies are also better at discriminating native-like conformations from non-native conformations.

Applications

Applications relevant to RNA structure modeling and design are available at rosetta_source/src/apps/public/rna

Algorithm

Input Files

You need one input files to run RNA Strcuture Modeling.

Density-Scoring Options

Result Interpretation

***Energy interpreter for low resolution silent output:
score     		                                   Final total score
rna_rg                                           Radius of gyration for RNA
rna_vdw                                          Low resolution clash check for RNA
rna_base_backbone                                Bases to 2'-OH, phosphates, etc.
rna_backbone_backbone                            2'-OH to 2'-OH, phosphates, etc.
rna_repulsive                                    Mainly phosphate-phosphate repulsion
rna_base_pair_pairwise                           Base-base interactions (Watson-Crick and non-Watson-Crick)
rna_base_pair                                    Base-base interactions (Watson-Crick and non-Watson-Crick)
rna_base_axis                                    Force base normals to be parallel
rna_base_stagger    				 Force base pairs to be in same plane
rna_base_stack                                   Stacking interactions
rna_base_stack_axis                              Stacking interactions should involve parallel bases.
atom_pair_constraint                             Harmonic constraints between atoms involved in Watson-Crick base
                                                 pairs specified by the user in the params file
rms                                              all-heavy-atom RMSD to the native structure

***Energy interpreter for fullatom silent output:
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
lk_nonpolar                                      Lazaridis-karplus solvation energy, over nonpolar atoms
hack_elec_rna_phos_phos                          Simple electrostatic repulsion term between phosphates
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
ch_bond                                          Carbon hydrogen bonds
geom_sol                                         Geometric Solvation energy for polar atoms
rna_torsion                                      RNA torsional potential.
atom_pair_constraint                             Harmonic constraints between atoms involved in Watson-Crick base pairs
                                                 specified by the user in the params file
angle_constraint                                 (not in use)
rms                                              all-heavy-atom RMSD to the native structure

***If you use the sample flag files, there are also three pdb file generated.
start.pdb:                                       Idealized, fully extended starting structure.
random.pdb:                                      Structure with randomized torsion angles.
S_0001.pdb:                                      Output of the rna denovo design.

References

  1. Das, R. and Baker, D. (2007), "Automated de novo prediction of native-like RNA tertiary structures", PNAS 104: 14664-14669.
  2. Das, R., Karanicolas, J., and Baker, D. (2008), "A high resolution force field for predicting and designing RNA noncanonical structure", submitted.

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