Proteins are some of the building blocks of organisms. They usually perform their functions by interacting with each other and forming protein complexes. A protein-protein interaction network is a graph that consists of proteins as vertices and their interactions as edges. Protein-protein interaction network alignment is very important in identifying protein complexes and predicting protein fun...

Despite our extensive knowledge about the rate of protein sequence evolution for thousands of genes in hundreds of species, the corresponding rate of protein function evolution is virtually unknown, especially at the genomic scale. This lack of knowledge is primarily because of the huge diversity in protein function and the consequent difficulty in gauging and comparing rates of protein functio...

In the last few years a large amount of protein interaction data has been collected and stored in public databases. The automatic analysis and management of such data can provide valuable information on the evolution of different organisms. To this aim, interaction data can be modelled as graphs where nodes represent cellular components and edges are associated to interactions. Such graphs are ...

Proteins carry out their functions by means of interaction. There are two major types of protein-protein interaction (PPI): obligate interaction and transient interaction. In this paper, residues with geographical information on the binding sites are used to discover association patterns for classifying protein interaction type. We use the support of a frequent pattern as its inference power. H...

The increasing availability of large-scale protein-protein interaction (PPI) data has made it possible to understand the basic components and organization of cell machinery from the network level. Many studies have shown that clustering protein interaction network (PIN) is an effective approach for identifying protein complexes or functional modules. A significant number of proteins in such PIN...

Recent advances in high-throughput laboratory techniques captured large-scale protein-protein interaction (PPI) data, making it possible to create a detailed map of protein interaction networks, and thus enable us to detect protein complexes from these PPI networks. However, most of the current state-of-the-art studies still have some problems, for instance, incapability of identifying overlapp...

Uncovering the signaling architecture in protein-protein interaction (PPI) can certainly benefit the understanding of disease mechanisms and promise to facilitate the therapeutic interventions. Therefore, it is important to reveal the signaling relationship from one protein to another in terms of activation and inhibition. In this study, we propose a new measurement to characterize the regulati...

Protein-protein interactions (PPIs) can be classified as permanent or transient based on their stability lifetime. Understanding the precise details of such protein will pave way for discovery inhibitors and understanding nature function PPIs. In present work, 43 relevant physicochemical, geometrical structural features were calculated a curated dataset from literature, comprising 402 protein-p...

The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. ...

With the availability of more and more genome-scale protein-protein interaction (PPI) networks, research interests gradually shift to Systematic Analysis on these large data sets. A key topic is to predict protein complexes in PPI networks by identifying clusters that are densely connected within themselves but sparsely connected with the rest of the network. In this paper, we present a new top...