First we do the preparation step program:

• preparation.ipynb, this step modifies our molecule by removing specific atoms and adding hydrogen.

Now first step:

• step1-interface-res.ipynb Here we find the contacts between residues in different chains as well as their distance

Now second step:

• step2-energy_evaluation.ipynb Here we calculate the energies of the protein: the energy of all the residues on the interface, Total energy binding energy
• alanine change, effect of replacing each interface residue with alanine
• We have three text files with the results of these programs

Now third step:

• step3-plot.Rmd This is the plot of out previous results

Finally fourth step

• step4_picture.psw To see this you have to download it because it is a pymol file, we arranged the structure of the protein on pymol and colored the residues depending on their importance.