An example with inputs using the crystal structure of inactive-state CXCR4 (PDB ID: 3odu) and code for analysis is in the 3odu_SymDock_Example folder. The symmetry definition file is present in the input folder, but can otherwise be made with the makes_symmetry_file.command in the input folder
Change PATH_TO_ROSETTA in SymDock_native_symmetry.cmd and Native_SymDock_flag. Run it to generate ~10,000 decoys.
Navigate to the SymDock_analysis_example folder and follow the steps in SymDock_Analysis.txt to analyze the symmetric docking results.
mOR input files are in the 6ddf_SymDock folder to generate symmetric dimer models of the active-state mOR structure (PDB ID: 6DDF).
An example is in the bArr_Docking/CXCR4_Arrestin_Example folder. Inputs can be prepped by aligning receptor models to the 4ZWJA_receptor.pdb complex in the prepare folder and using the 8 arrestin structures (ar1-8.pdb). Change the PATH_TO_ROSETTA in the bArr_dock.cmd and in input/dock_flag. Generate ~1000 decoys for each arrestin model to get ~8000 total decoys. Select the top 1% by interface score and cluster for native-like finger loop position.
examples are in the Gi_Docking/CXCR4_Gi_example. Change the PATH_TO_ROSETTA in the Gi_dock.cmd and generate ~10,000 decoys. Select the top interface scoring model with native-like G protein C-terminal helix position among the top 1% interface scoring decoys.
Sequences in Fasta folder were used as input for ColabFold (v1.4).