From the manuscript:
Terra Sztain,† Joshua C. Corpuz,† Thomas G. Bartholow, Javier O. Sanlley Hernandez, Ziran Jiang, Desirae A. Mellor, Graham W. Heberlig, James J. La Clair, J. Andrew McCammon*, and Michael D. Burkart*
Rosetta version 3.9 was used throughout.
Loops not resolved in the crystal structure PDB 6O6E were modeled with rosetta. The file 606E-2fad.pdb contains the PltF-AcpP input structure aligned in PyMOL as described in the manuscript.
The remodel file was generated by running:
/PATH_TO_ROSETTA/rosetta/3.9/tools/remodel/getBluePrintFromCoords.pl -pdbfile ./606E-2fad.pdb -chain A > ./606E-2fad.remodel
The resulting 606E.remodel file was modified as follows:
...
11 V .
12 K L PIKAA K
0 x L PIKAA K
0 x L PIKAA P
0 x L PIKAA G
13 S L PIKAA S
14 S .
...
Loop remodeling was run:
/PATH_TO_ROSETTA/rosetta/3.9/main/source/bin/remodel.static.linuxgccrelease -database /PATH_TO_ROSETTA/rosetta/3.9/main/database/ -s ./606E-2fad.pdb -run:chain A -remodel:use_blueprint_sequence -remodel:blueprint ./606E-2fad.remodel -ex1 -ex2 -use_input_sc -overwrite
/PATH_TO_ROSETTA/rosetta/3.9/main/source/bin/relax.static.linuxgccrelease -database /PATH_TO_ROSETTA/rosetta/3.9/main/database/ -relax:fast -s ./606E-2fad_loop_modeled.pdb -ex1 -ex2 -use_input_sc
The interface_design.xml file was modified from this Rosetta Demo.
/PATH_TO_ROSETTA/rosetta/3.9/main/source/bin/rosetta_scripts.static.linuxgccrelease -s ./606E-2fad_loop_modeled_relaxed.pdb -database /PATH_TO_ROSETTA/rosetta/3.9/main/database/ -parser:protocol ./interface_design.xml -ex1 -ex2 -nstruct 1000 -overwrite
For modifying the score function, the following commandline flag was added to the above:
-score:set_weights fa_elec 1.5
Terms and weights for the REF2015 score function can be found here.
To generate input list of structures for analysis:
ls 606E-2fad_loop_modeled_relaxed_* > list.txt
The python script SequenceProfile.py was used to analyze the sequence profile:
python2.7 SequenceProfile.py -l list.txt -t 606E-2fad_loop_modeled_relaxed.pdb
To generate point mutant pdb structures, the mutate.xml file was used by running:
/PATH_TO_ROSETTA/rosetta/3.9/main/source/bin/rosetta_scripts.static.linuxgccrelease -s ./606E-2fad_loop_modeled_relaxed.pdb -database /PATH_TO_ROSETTA/rosetta/3.9/main/database/ -parser:protocol ./mutate.xml -ex1 -ex2 -nstruct 1
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