Author: Rhiju Das
This document updates documentation written in 2008 by Rhiju Das (rhiju [at] stanford.edu) into the latest documentation format. Last update: April 2011.
The central code for the rna_design application is in
apps/public/rna/rna_design.cc with core routines run through the Rosetta packer.
For a 'minimal' demo example of RNA design:
demos/public/RNA_Design [in the release version]
There is also a nice server available for this code at rnaredesign.stanford.edu
(Reprint available at http://daslab.stanford.edu/pubs.html ).
This code is intended to carry out fixed backbone design of RNA sequences given an input backbone.
This application carries out combinatorial optimization of nucleobase type and conformation along with 2'-OH torsions, in the context of a pre-specified RNA backbone. It is very similar to the Rosetta fixed-backbone protein design algorithm, and has been used to test the new Rosetta RNA potential. Unfortunately, it is not presently very optimized for speed; the precalculation of rotamer energies takes a while. Runs on RNA backbones longer than ~ten nucleotides take many minutes or hours; algorithm improvements implemented in future releases will greatly speed this up.
Just the PDB file with desired backbone.
rna_design.<exe> -s chunk001_uucg_RNA.pdb -nstruct 3 -ex1:level 4 -dump -score:weights farna/rna_hires.wts
This demo redesigns a 'UUCG' tetraloop on a single-base pair RNA 'helix', as a small 6-nucleotide test case. As illustration, only 3 designs are output. It takes about 15 seconds to run. The typical sequence output is cuuggg (native is cuucgg).
-in:file:s Name(s) of single PDB file(s) to process. [FileVector] -nstruct Number of times to process each input PDB. [Integer] -ex1:level <n> Use extra chi1 sub-rotamers for all residues that pass the extrachi_cutoff. [Boolean] The integers that follow the ex flags specify the pattern for chi dihedral angle sampling. There are currently 8 options; they all include the original chi dihedral angle No. 4 means: EX_TWO_HALF_STEP_STDDEVS [-1,-1/2,0,1/2,1 standard deviations]. -dump Generate pdb output,default:false. [Boolean] -score:weights farna/rna_hires.wts Name of weights file, default is standard. [String] -sample_chi Sample chi (glycosidic torsion angle). -disable_o2star_rotamers Turn off sampling of 2'-OH proton position. -database (Optional) Path to rosetta databases. Default is based on location of rosetta executables. [PathVector]
The most common question we get is on what the terms in the 'SCORE lines' of silent files mean. Here's a brief rundown, with more explanation in the papers cited above.
***Energy interpreter for fullatom silent output: score Final total score fa_atr lennard-jones attractive fa_rep lennard-jones repulsive fa_intra_rep Lennard-jones repulsive between atoms in the same residue lk_nonpolar lazaridis-karplus non-polar solvation energy 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 and sidechain-backbone hydrogen bond energy ch_bond Carbon hydrogen bonds geom_sol Geometric Solvation energy for polar atoms rna_torsion RNA torsional potential. atom_pair_constraint Atom pair distance constraints score? angle_constraint (not in use) rms rmsd
If you use the sample flag files, there are also other output files generated.
start.pdb: Idealized structure S_000*.pdb: Output of the rna denovo design. chunk001_uucg_RNA.sequence_recovery.txt: This is a simple report for design identity of each RNA residue and structure. chunk001_uucg_RNA.pack.txt: Total score and sequence for each output model chunk001_uucg_RNA.pack.out: Scores (with breakdown by score component) for each re-designed sequence