This Figure documents the docking protocol used for this study. Individual docking trajectories are very fast (order of 30s per trajectory) and are independent, so many-processor MPI is suggested. Rosetta command line: /path/to/rosetta/source/bin/rosetta_scripts.release @options The options file consists of: #begin options #database path -database /path/to/rosetta/database #input path; pdblist is an endline-delimited list of paths to pdb files (one PDB per line) -l pdblist #perform 2 repacks but only output the best each cycle -ndruns 2 #allow 100 attempts to pass docking filters -jd2:ntrials 100 #perform 750 trajectories per input -nstruct 750 #docking settings -docking:dock_pert 2 4 #minimization settings -run::min_type dfpmin_armijo_nonmonotone #packing settings -ex1 -ex2 -use_input_sc #scoring corrections, probably superseded by the time of publication -no_his_his_pairE -corrections::score::score12prime #write the rosetta version and options to the log file -options:user -run:version #this exclusion reduces memory use but is not important -chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer protein_cutpoint_upper protein_cutpoint_lower VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm #output controls -out:file:silent docking_lrf.out -out:file:silent_struct_type binary #quiet mode -mute all #script to define docking -parser:protocol lrf_docking.xml #end options The lrf_docking.xml file controls the docking protocol. #begin lrf_docking.xml #end lrf_docking.xml