5. Short protein-protein docking research project: a comparative bo...

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5. Short protein-protein docking research project: a comparative bound and unbound protein-protein docking exercise using the barnase-barstar complex.

a. Download 1brs.pdb from the Protein Data Bank (PDB)
b. Save chains A and B as a single file (1brs_ab.pdb)
c. Find a crystal structure of the unbound conformation of barnase
d. Find a crystal structure of the unbound conformation of barstar

e. Use the HEX docking server to re-dock the bound receptor protein and ligand protein conformations of 1BRS (chains A and B); download and save the top 10 HEX predictions for further analysis.

f. a. Use the HEX docking server to dock the unbound receptor protein and ligand protein conformations of 1BRS (chains A and B); download and save the top 10 HEX predictions for further analysis.

g. Use the Deep View "magic fit tool" (Swiss PDB Viewer) to quantitatively compare your bound re-docking and unbound docking predictions with the experimental 1brs.pdb complex structure.

Based on the results, fill in the following two tables.

Bound docking pose    C-alpha RMSD    All-atom RMSD      Number of interface h-bonds
1
2
3
4
5
Unbound docking pose    C-alpha RMSD    All-atom RMSD    Number of interface h-bonds
1
2
3
4
5
h. For the bound docking study, did HEX docking identify a top 5 pose within 2.0 Å C-alpha rmsd of the x-ray complex?
i. For the unbound docking study, did HEX docking identify a top 5 pose within 2.0 Å C-alpha rmsd of the x-ray complex?

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