1. USAGE

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To run the Software Package from the command line using default parameters, Run the run_predict_binding.py script as:

./run_predict_binding.py XXXX.pdb

2. INPUT

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The three dimensional coordinates of the atomic positions of the protein complex should be given in a PDB format. Place the PDB files in the 'input' directory of the package.

3. OUTPUT

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After a successful run of the program, the corresponding output files are generated in the 'output' directory. For each complex, two text files will be generated -

1. XXXX_scores.out - Contains the prediction and other metrics like z-score
2. XXXX_respairs.out - Contains the residue pairs comprising the interface

In case the Alanine Scanning flag is provided, an additional file will be generated, 3. XXXX_alascan.out - Contains the residues which upon mutation might destabilize the interaction

4. EXAMPLES

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Examples for the input and output files are provided in the 'examples' directory

5. ADDITIONAL PARAMETERS

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Optional flags that can be turned on - USAGE:

./run_predict_binding.py XXXX.pdb -d 8.0 -t mm

1. Distance threshold for interaction definition: -d, --cutoff, choices = {4.0, 6.0, 8.0} NOTE: Default value = 4.0

2. Types of interacting atoms between residues: -t, --intertype, choices = {'all', 'mm', 'ms', 'ss'} NOTE: Default value = ss all - Interactions between all atoms mm - Interactions between main chain atoms ms - Interactions between main chain atoms and side chain atoms ss - Interactions between side chain atoms

3. To specify your own 20x20 matrix for residue-pair scores: -cp, --custom_pot, file NOTE: The custom potential should be in the format of a .csv file with the residue_pair in first column and the corresponding score in the second column. Example file provided in the 'examples' directory (custom_pot.csv)

4. To perform Alanine Scanning with the default potential: -alscn, --alascan, choices = {'0', 1', '2', '3'} NOTE: Default value = '0' 0 - Do not perform Alanine Scanning 1 - Mutate all the residues on the interface to Alanine 2 - Mutate all the residues on the interface to every other residue 3 - Mutate a given list of residues to every other residue (residues to be provided in a separate file)

   *NOTE: In case mode '3' is selected, a separate file containing the residues to be mutated should be provided in the 'input' directory. An example file is given in the 'examples' directory (4pza_alscan_input.txt).

5. In case of multimers, specify particular interfaces, -p1, -p2, --protein_1, --protein_2

6. To specify a name for the output files, -o, --outfile

This help can be accessed on the command line using: ./run_predict_binding.py -h or ./run_predict_binding.py --help

6. SOURCE CODE

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All the scripts for the package can be found in the 'scripts' directory.

7. LICENSE

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Please refer to COPYING.txt for the full license or COPYING_LESSER.txt for a condensed version.