The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: MEMBRANES STRUCTURE_PREDICTION
Bold text means that these files and/or this information is provided.
Italicized text means that this material will NOT be conducted during the workshop.
Fixed width text means you should type the command into your terminal.
If you want to try making files that already exist (e.g., input files), write them to a different directory!
Preparation for running MembraneAbinitio
Prepare your working directory. You will work in this directory for the rest of the tutorial.
Create a directory in the MembraneAbinitio/ directory called my_files and switch to that directory.
$> mkdir my_files $> cd my_files
Save your protein sequence to a file using FASTA format.
The BRD4A.fasta file is provided for you in the
$> cp ../input_files/BRD4A.fasta .
Generate the spanfile.
$> cp ../input_files/BRD4A.octopus . $> $ROSETTA3/src/apps/public/membrane_abinitio/octopus2span.pl BRD4A.octopus > BRD4A.span
Generate the LIPS lipophlicity file http://tanto.bioengr.uic.edu/lips/ (Adamian and Liang, BMC Struct. Biol., 2006).
Note: Can only generate this file if have BLAST and NR database installed. To use the LIPS server, you must have a multiple sequence alignment. We will not run this script during the workshop! See the example below:
> $ROSETTA3/src/apps/public/membrane_abinitio/run_lips.pl BRD4A.fasta BRD4A.span /blast/bin/blastpgp /nr_database $ROSETTA3/src/apps/public/membrane_abinitio/alignblast.pl
Prepare fragment libraries.
The BRD4 fragment files (aaBRD4A03_05.200_v1_3 and aaBRD4A09_05.200_v1_3) are already provided in the
$> cp ../input_files/aaBRD4A03_05.200_v1_3 ../input_files/aaBRD4A09_05.200_v1_3 .
Prepare the options file.
The BRD4_mem_abrlx.options file is already provided in the
$> cp ../input_files//BRD4_mem_abrlx.options .
Prepare the rigid file.
The BRD4A_TM_rms.txt file is already provided in the
$> cp ../input_files/BRD4A_TM_rms.txt .
BRD4A_TM_rms.txt is a file containing the residues over which you want to compute the CA-RMSD (the membrane-spanning regions in this case). It has the format:
RIGID 6 26 RIGID 31 51 RIGID 58 78 RIGID 97 117
Copy over other necessary files.
$> cp ../input_files/1PY6A.pdb .
Running the MembraneAbinitio application.
Execute the following command line.
$> $ROSETTA3/bin/membrane_abinitio2.default.linuxgccrelease @BRD4_mem_abrlx.options
NOTE: This will take 3-5 minutes per structure
$> cd ..
Analyze your data.
Example data is provided for you in the
For practice, we will be analyzing data that has already been generated.
Create a directory for analysis of your data and switch into that directory.
$> mkdir data_analysis $> cd data_analysis
Copy the files from the example_data directory.
$> cp ../example_data/* .
Combing and extracting silent files and extracting PDBs of membrane proteins is slightly different than for soluble proteins, but is a very similar process as that described in the de novo folding tutorial. To combine silent files:
$> $ROSETTA3/bin/combine_silent.default.linuxgccrelease -in:file:silent BRD4A*.out -in:file:silent_struct_type binary -in:file:residue_type_set centroid -in:file:spanfile BRD4A.span -score:weights score_membrane -out:file:silent BRD4A_mem_abrlx_all.out -out:file:silent_struct_type binary -out:file:residue_type_set centroid
Find the lowest-scoring models.
$> python $ROSETTA_TOOLS/protein_tools/scripts/score_scatter_plot.py --x_axis rms_TM --y_axis score --silent BRD4A_mem_abrlx_all.out BRD4A_mem_abrlx_all_score_vs_rmsd.table $> sort -nk3 BRD4A_mem_abrlx_all_score_vs_rmsd.table | head -n10
To extract PDBs:
$> $ROSETTA3/score_jd2.default.linuxgccrelease -in:file:silent BRD4A_mem_abrlx_all.out -in:file:tags S_00000058_1\
-in:file:silent_struct_type binary -in:file:residue_type_set centroid -in:file:spanfile BRD4A.span -score:weights score_membrane -out:output -out:pdb -out:file:residue_type_set centroid -in:file:tags S_00000044_1_0001_0001 S_00000044_1_0001 S_00000077_1_0001 S_00000130_1_0001 S_00000144_1_0001_0001 S_00000144_1_0001 S_00000168_1_0001_0001 S_00000168_1_0001 S_00000187_1_0001 S_00000247_1_0001
Generate score vs. RMSD plots etc. The scripts to make an XY-scatter plot for membrane proteins are called score_vs_rmsTM.R and score_vs_rmsTM_low.R. These scripts are found in the ~/rosetta_workshop/tutorials/protein_folding/scripts directory. If you want to rescore your models and compute the RMSD against the lowest-scoring model, repeat the previous step with the following changes:
$> $ROSETTA/bin/score_jd2.default.linuxgccrelease -in:file:native S_00000044_1_0001_0001.pdb -in:file:silent BRD4A_mem_abrlx_all.out -in:file:silent_struct_type binary -in:file:residue_type_set centroid -in:file:spanfile BRD4A.span -score:weights score_membrane -out:file:residue_type_set centroid -out:file:silent BRD4A_mem_abrlx_all_rescore.out -out:file:silent_struct_type binary -evaluation:rmsd NATIVE TM_low ../input_files/BRD4A_TM_rms.txt
OPTIONAL: Relaxing Membrane Proteins in Rosetta (will not be covered in tutorial)
Folding membrane proteins with the topology broker with restraints
The example input and output files, as well as the command line and analysis files, can be found in