1. Download the source package

Download the package

2. Extract PIZSA_v2_source.tar.gz package, execute the following command on the command prompt:

tar -xf PIZSA_v2_source.tar.gz --> This will create a directory in the name of 'PIZSA_v2_source'

Most systems have the appropriate extraction program installed by default but if the 'tar' program is not installed then please install it on your system.

3. Test the pizsa program: First change the directory to the extracted folder (using (A)) and then execute the command in (B)

(A) cd PIZSA_v2_source/ -- > This directory was created in the step-2 above.

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

(B) ./run_predict_binding.py XXXX.pdb

4. Output file description:

After a successful run of the program, the corresponding output files are generated in the directory where the input PDB file was present. For each complex, two text files will be generated -

1. XXXX_scores.txt- This file lists out all the parameters used for the given run and the prediction. All other important metrics towards making the prediction are reported here.

2. XXXX_respairs.txt- This file lists all the amino acid residue pairs that constitute the interfaces in the given protein complex. The residues are split into columns based on the subunits. The final column shows the contribution of the given pair towards the score of the complex.

FORMAT: The entries in the repairs.txt file are in column output format that have the following convention,

"XXX:YYY:A, where XXX = residue number, YYY = residue type & A = protein subunit."

For example - 321:ALA:A is the Alanine at position 321 of the subunit A

In case the Mutational Analysis flag is provided, an additional file will be generated,

3. XXXX_mutscan.txt- This file contains the results of the mutational analysis. The most important residues are listed in a ranked order list. The last column shows the magnitude of change in scores upon mutagenesis. Positive values indicate the mutation is destabilising whereas Negative values indicate the mutation is stabilizing.

Please read the README file for full description of PIZSA command line flags, help and examples.