Protein-protein docking with Rosetta

Purpose: To predict the binding mode between two protein structures, or a protein with a peptide.

1. Preparation
In your working directory, you will need the following (can be copied from /sb/demo/rosetta/dock ): 1. One pdb file containing the structures of your two docking partners. The pdbfile should be 'cleaned' to contain only ATOM, TER, and END records, have no missing residues, and be two single chains. There is an example file called separated.pdb, that contains alpha amylase and a cognate antibody fragment. 2. A paths file telling Rosetta where to look for data libraries, where to output the models, scores, etc. 3. A subdirectory named decoys to hold the resulting models. 4. A subdirectory named scores to hold the scores for each result. 5. The rosetta.gcc executable program (unless it's already in your path). 6. You may also need to run 'sbset meilergroup' to initialize your working environment.

2. Conduct the naive docking run

1. Type rosetta.gcc to see a list of arguments that the program accepts 2. This is the command to dock your structures:
rosetta.gcc aa foo2 1 -dock -s separated.pdb -randomize2 -nstruct 1000 >& aa_test.log rosetta.gcc bb foo2 1 -dock -s separated.pdb -randomize1 -randomize2 -nstruct 10000 >& bb_test.log rosetta.gcc cc e1q1 _ -dock -s X.pdb -randomize1 -randomize2 -nstruct 1000>& out.txt rosetta.gcc re e1q1 1 -dock -s X.pdb -randomize2 -nstruct 5000 >& re_test.log & rosetta.gcc op e1q1 1 -dock -s X.pdb -randomize2 -nstruct 5000 >& op_test.log &

3. Meaning of arguments: 1. 'aa' is an arbitrary 2-letter code used to label your output files 2. 'e1q1' is a required pdbfile basename. It should match your input structure's name. If you use a constraints file or other supplementary input files, it must correspond to those. 3. '_' is a required chainID digit. If you don't use the -randomize flags, it determines which chain is perturbed. 4. '-s filename.pdb' specifies the starting structure 5. '-nstruct' is number of decoys generated per input file

3. Perform docking with biological constraints

1. You can create two constraint files: a site-constraint (basename.cst) and a distance-constraint (basename.dst). For an example of the file format, see the example directory. 2. This is the command to dock your structures:
rosetta.gcc aa foo2 1 -dock -s separated.pdb -randomize2 -nstruct 1000 > & aa_test.log

4. Examine results
1. Read the log, the scores file, and examine the models produced in the /decoys/ directory with a text editor. 2. Load the models into your favorite viewing program (chimera, pymol, etc) and compare them with the native ubiquitin structure (1ubi.pdf). What is the biggest difference between the structures?

5. Other resources
1. The paper describing docking using Rosetta is this one: Protein-Protein Docking with Simultaneous Optimization of Rigid Body Displacement and Side Chain Conformations, J.J. Gray, S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl and D. Baker, J. Mol. Biol., 331(1), 281-299

2003. 2. There is a good docking tutorial available on the web here: http://graylab.jhu.edu/~mdaily/tutorial/basics_main.html
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