logo logo logo
Barnase barstar docking

This script uses all pdb structures and grids in data_grid/. You need to run at least one time the script in prepare_grid_and_ecm/ to generate the grids and effective charges in this folder.

If you want more information about this step, refer to the tutorial in examples/Tutorial_SDA7/.

Running the examples

cd bnbs_docking/

You can check that the output files are similar to the ones generated at HITS in bnbs_docking_hits/

Note: the script run_clusterDPipe.sh will be executed by the main script, but feel free to use it as a template.

Details of the script

The script will generate the most favorable docking positions between barnase and barstar in 2 ways:

In both cases, the complexes saved during the SDA runs are subsequently clustered and 5 representative configurations are generated.

Description of the results

The results of the clustering are in their respective subfolders, in the file out_clustering.
You can find all the information about these outputs in the documentation of the cluster program.

In both simulations, the first clusters are the most populated, with more than half of the complexes.
Furthermore, they have the lowest interaction energy, and the minimum RMSD (computed from p2_noh.pdb, which is the crystal structure).

The figure below shows the crystal structure of the barnase-barstar complex, and the representatives of the first clusters for the 2 simulations.

snap docking
   Yellow: barnase (solute 1)
   Red: barstar (solute 2) - position in the crystal structure of the complex
   Blue: Representive from simulations with only the electrostatic interaction (RMSD 6 Å)
   Green: Representative from simulations with all energy terms (RMSD 5 Å)

[Back to Main Documentation]