The scripts and input files that accompany this demo can be found in the demos/public directory of the Rosetta weekly releases.



Rhiju Das,

Edited in 2016 by Parisa Hosseinzadeh to enable automatic testing of demos.

Brief Description

Solve structure of an RNA loop or motif in the context of a starting structure.


Ab initio and comparative modeling of biopolymers (RNA, protein, protein/RNA) often involves solving well-defined small puzzles (4 to 20 residues), like RNA aptamers, RNA tertiary contacts, and RNA/protein interactions. If these problems have torsional combinations that have not been seen previously or are not captured by coarse-grained potentials, most Rosetta approaches will fail to recover their structures. This app implements a stepwise ansatz, originally developed as a 'stepwise assembly' enumeration that was not reliant on fragments or coarse-grained modeling stages, but was computationally expensive. The new mode is a stepwise monte carlo, a stochastic version of stepwise assembly.


Example Rosetta Command Line ($ROSETTA3= path-to-Rosetta/main/source)

$> $ROSETTA3/bin/stepwise.default.linuxgccrelease -in:file:fasta rosetta_inputs/1zih.fasta -s rosetta_inputs/start_helix.pdb  -out:file:silent swm_rebuild.out -extra_min_res 4 9 -score:rna_torsion_potential RNA11_based_new -chemical::enlarge_H_lj -score:weights stepwise/rna/rna_res_level_energy4.wts -restore_talaris_behavior
Currently, we are mainly using a scorefunction with a more stringent torsional and repulsive potential, enabled by flags -score:rna_torsion_potential RNA11_based_new -chemical::enlarge_H_lj.

To get out models (here from a test case). You can see one example of structure in 1zih_RNA.pdb in the rosetta_inputs directory.

$> $ROSETTA3/bin/extract_pdbs.default.linuxgccrelease -silent rosetta_inputs/swm_rebuild.out 

(Or use which can be installed via tools/rna_tools/.)

Example Rosetta Command Line for Design

Simply use a fasta file that has n's at positions you want to design.

$> $ROSETTA3/bin/stepwise.default.linuxgccrelease -in:file:fasta rosetta_inputs/NNNN.fasta -s rosetta_inputs/start_helix.pdb  -out:file:silent swm_design.out -extra_min_res 4 9 -score:weights stepwise/rna/rna_res_level_energy4.wts -restore_talaris_behavior