Introduction and Motivation
PRInS is a tool that is able to detect ‘important’ aminoacids using only the tertiary structure of a protein. The idea behind PRInS is kind of unusual, but quite simple.
The text below summarizes the motivation:
Intra- and inter-protein interactions depend on the involved aminoacids. Energetically favorable interactions have been preserved during evolution, and thus they are abundant in nature. On the other hand, most energetically unfavorable interactions have been dismissed. Thus, maintaining an unfavorable interaction suggests a cause beyond energy optimization. Such a cause may be functional; this means that the specific interaction has an important functional role that forces its preservation during evolution. Assuming that unexpectedly rare interactions are energetically unfavorable, we developed an algorithm to detect them using protein tertiary structures. The algorithm, called PrInS (Protein Interaction Statistics), is trained with a set of known protein tertiary structures. Then, a protein of interest is scanned and interactions are scored based on their frequency in the training set.
Download the code from here
Download the data used in Jha et al. 2011 from here.
Figure 1: Each residue is colored according to its score. Red residues have a higher score than blue residues. Upper and lower boundaries denote the membrane.