The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: STRUCTURE_PREDICTION DENOVO NUCLEIC_ACIDS RNA INTERFACES
Written in April 2018 by Kalli Kappel (kappel at stanford dot edu).
This demo shows how to model the 3D structure of an RNA-protein complex starting from a protein structure and RNA sequence.
fasta.txtis a file specifying the sequence of the RNA-protein complex.
secstruct.txtis a text file specifying the secondary structure for the RNA-protein complex in dot-bracket notation. Secondary structure for the protein should be specified by dots. The secondary structure should be the same length as the sequence found in the fasta file.
unbound_protein.pdbis the unbound protein structure (you could alternatively use a homology model of the protein or the bound protein structure if it's known). This will be treated as a rigid body throughout the run. This structure must contain all of the protein residues that are in your
fasta.txtfile (this protocol does not build protein residues from scratch).
RNA_helix.pdbis a structure of a 3-residue helix (generated with
rna_helix.pyin RNA tools). This will be treated as a rigid body throughout the run.
unbound_protein_and_RNA.pdbis a structure containing both the unbound protein structure and the RNA helix. Putting both structures in the same file will fix the relative rigid-body orientation of the two and no docking moves will be performed.
flagscontains all the flags for the run (or alternatively
flags_no_dockfor the run where the RNA helix is fixed relative to the protein). The options in this flags file are:
-fasta fasta.txt: specifies the fasta file to use (
-secstruct_file secstruct.txt: specifies the file containing the secondary structure to use (
-s unbound_protein.pdb RNA_helix.pdb: the input structures for the run. These will be treated as rigid bodies.
-new_fold_tree_initializer true: sets up the kinematics for the problem (this flag is strongly recommended for RNA-protein modeling).
-minimize_rna false: do low-resolution modeling only.
-nstruct 5: the number of structures to build. Typically, you will want to build a total of several thousand structures.
-out:file:silent 2qux_fold_and_dock.out: The name of the silent file that will be written (this will contain all of the predicted structures in a compressed format).
rna:denovo:lores_scorefxn rna/denovo/rna_lores_with_rnp_aug.wts: the low-resolution score function to use (
-cycles 1000: The number of Monte Carlo cycles per structure. Recommended: ~2 times the number of RNA residues that are being modeled.
-rna_protein_docking true: Do RNA-protein docking moves.
-convert_protein_CEN false: Don't convert protein residues to centroid mode during the run (the low-resolution score function will still be used though).
-FA_low_res_rnp_scoring true: Use the version of the low-resolution score function based on the actual sidechain centroid positions, rather than the Rosetta centroid positions.
-ramp_rnp_vdw true: Gradually increase the rnp_vdw weight throughout the run.
-docking_move_size 1.0: Use regular docking moves.
-no_filters: Don't use any filters throughout the run (not recommended for regular runs).
Models of the RNA-protein complex will be built with the Rosetta fold-and-dock method, which combines FARNA RNA folding with RNA-protein docking. First, type:
This will take several minutes to run and will generate 5 structures. For a normal run, it is typically best to generate several thousand structures.
The final structures will be found in the silent file
To extract PDB files from the silent file, type:
extract_lowscore_decoys.py 2qux_fold_and_dock.out 5
This will create 5 PDB files named 2qux_fold_and_dock.out.1.pdb, 2qux_fold_and_dock.out.2.pdb, etc.
Alternatively, to build models of the RNA-protein complex keeping the rigid-body orientation of the RNA helix and the protein fixed, first type:
Again, this will take several minutes to run and will generate 5 structures in a silent file named
2qux_fold_and_dock_fix_rigid.out. To extract PDB files from the silent file, type:
extract_lowscore_decoys.py 2qux_fold_and_dock_fix_rigid.out 5
These structures should be viewed in a molecular graphics program of your choice, e.g. Pymol.
For reference, example output for this demo is provided in the
See additional documentation here.