Modeling the topology of protein interaction networks

TL;DR

This paper introduces a two-step model that replicates key topological features of protein interaction networks, such as degree distribution and clustering, providing insights into their underlying structure and allowing system-specific fitting.

Contribution

The novel two-step model accurately reproduces the topological properties of protein interaction networks and can be tuned to fit different biological systems.

Findings

Networks exhibit small world features, not scale-free.

Model replicates degree and cluster size distributions.

Single parameter tuning fits various biological networks.

Abstract

A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein networks is not well understood yet. Here we present a two-step model, which generates clusters with the same topological properties as networks for protein-protein interactions, namely, the same degree distribution, cluster size distribution, clustering coefficient and shortest path length. The biological and model networks are not scale free but exhibit small world features. The model allows the fitting of different biological systems by tuning a single parameter.