ﻻ يوجد ملخص باللغة العربية
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation but also the higher level organization of the cell. With the advent of high-throughput techniques in molecular biology, significant amount of physical interaction data has been cataloged from organisms such as yeast, which has in turn fueled computational approaches to systematically mine complexes from the network of physical interactions among proteins (PPI network). In this survey, we review, classify and evaluate some of the key computational methods developed till date for the identification of protein complexes from PPI networks. We present two insightful taxonomies that reflect how these methods have evolved over the years towards improving automated complex prediction. We also discuss some open challenges facing accurate reconstruction of complexes, the crucial ones being presence of high proportion of errors and noise in current high-throughput datasets and some key aspects overlooked by current complex detection methods. We hope this review will not only help to condense the history of computational complex detection for easy reference, but also provide valuable insights to drive further research in this area.
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserve
The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access genes co-expression patterns has moved the attention from the study of single prote
Recently, the structural controllability theory has been introduced to analyze the Protein-Protein Interaction (PPI) network. The indispensable nodes, which their removal increase the number of driver nodes to control the network, are found essential
In protein-protein interaction networks certain topological properties appear to be recurrent: networks maps are considered scale-free. It is possible that this topology is reflected in the protein structure. In this paper we investigate the role of
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help in the iden