A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

Abstract

The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.

Figure 1:

An example of protein–protein interfaces (interface region between p53 and its binding protein 53BP2).

Figure 2:

(A) HRAS interaction network visualized by STRING [122]. (B) The predicted interacting residues of HRAS (1bkd_R) using SPPIDER and PPI-Pred are displayed as spheres in white and silver color, respectively. The black spheres represent the residues that are common to both web servers. Predictions of SPPIDER and PPI-Pred web servers overlap both Switch I and Switch II regions of HRAS.