DeNovoHeterodimers

To generate heterodimer backboens with the heptad padding method

1. For initial heptad sampling, run setup_parallel.sh which calls initial_HBNet_search.xml
2. To generate heptad chain ordering varints and prepare for TMalign, run "for j in cat <list>;do cd $j;mkdir middles sides;for i in *pdb;do python heptad_padding.py $i $i <layer (2, 3, or 5)>;done;cd ../;done &"
3. Use perl ../bob.pl >p_do to generate run scripts for TMalign
4. sh process_after_devshm_tmalign.sh to filter for good TMalign-ed heptads onto backbones
5. sh PAD3_wrapper.sh *filtered.txt <number of residues per repeat (7, 11, 9 (because only sampling 9 residues for 5layer))> >log &   #this pads heptads into 3-network bundles

Loop closure

rosetta_scripts.hdf5.linuxgccrelease @loop_closure.flags

Final design

rosetta_scripts.hdf5.linuxgccrelease @heterodimer_final_design_only_design.flags -in:file:s $in_pdb

Native MS data analysis

1. To identify exchanged monomers: python native_MS_mixing_data_analysis.py mass_tolerance time_cutoff ms_list CID_mass_list theoretical_mass_list
2. To quantify exchanged monomers: python native_MS_mixing_data_quantitation.py theoretical_mass_list Non-denaturing_data1 Non-denaturing_data2 Denaturing_data1 Denaturing_data2

Script for NUS processing (4D-HNCH-TOCSY)

NMR_process.sh

Rosetta xml for scoring designs

scoring_script.xml