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Strategy: A protein-protein docking has been carried out to obtain an interaction model for the SspB adaptor protein and the protease subunit ClpX. This interaction model would be the first step in the development of a complete real structural model for the degradation process of a target protein by this protease system.

Procedure:

1. Obtain a pdb model for the SspB and ClpX proteins. In the case of SspB, no pdb model was available for this protein in the RCSB Protein Data Bank (PDB), so the protein homology modeling server Swiss Model and CPHmodels 3.0 server were used to obtain a structural model of this protein. However, for ClpX protein several pdb 3D files were available and the largest one was chosen (PDB entry 3hte).

2. Run the Hex protein-protein Docking server. A shape complementarity approach was chosen.

3. Analyse the docking results. RasMol 2.7.5. and Jmol 12.0 molecule viewers were used.