Structure‐based protein‐protein interaction networks and drug design

Abstract

Proteins carry out their functions by interacting with other proteins and small molecules, forming a complex interaction network. In this review, we briefly introduce classical graph theory based protein-protein interaction networks. We also describe the commonly used experimental methods to construct these networks, and the insights that can be gained from these networks. We then discuss the recent transition from graph theory based networks to structure based protein-protein interaction networks and the advantages of the latter over the former, using two networks as examples. We further discuss the usefulness of structure based protein-protein interaction networks for drug discovery, with a special emphasis on drug repositioning.

A Least Square Method Based Model for Identifying Protein Complexes in Protein-Protein Interaction Network

“…Combining dynamic information such as expression profiles can infer the dynamic properties of protein-protein interactions under different time points or various conditions [ 1 , 30 ]. On the other hand, when two or more proteins form a complex, some interface information as physical folds [ 31 ], biochemical properties [ 32 ], and posttranslation modifications [ 33 ] is very important to the complex formation. In the future, based on PLSMC, we will study the identification of protein complexes from dynamic protein-protein interaction networks and interface datasets.…”

Squeeze flow rheometry as a novel tool for the characterization of highly concentrated protein solutions

“…Due to the complexity of the system one approach has been to study the different physical and chemical parameters, which influence the aggregation process, separately. Step by step different interaction theories and influencing parameters were evaluated (Naveed and Han, ; Rao et al, ; Teeter, ). Kumar et al () analyzed the impact of short and long range forces on protein aggregation under varying conditions.…”

“…Step by step different interaction theories and influencing parameters were evaluated (Naveed and Han, 2013;Rao et al, 2014;Teeter, 1991). Kumar et al (2011) analyzed the impact of short and long range forces on protein aggregation under varying conditions.…”