Predicting Protein Interaction Sites Using PITHIA

Several proteins work independently, but the majority work together to maintain the functions of the cell. Thus, it is crucial to know the interaction sites that facilitate protein–protein interactions. The development of effective computational methods is essential because experimental methods are expensive and time-consuming. This chapter is a guide to predicting protein interaction sites using the program “PITHIA.” First, some installation guides are presented, followed by descriptions of input file formats. Afterward, PITHIA’s commands and options are outlined with examples. Moreover, some notes are provided on how to extend PITHIA’s installation and usage.