Many proteins are known to perform their own functions when they form particular groups of proteins, called protein complexes. With the advent of large-scale protein-protein interaction (PPI) studies, it has been a challenging problem in systems biology to predict protein complexes from PPIs. In this paper, we propose a novel method, called Repeated Simulated Annealing of Partitions of Proteins...

Characterizing the activating and inhibiting effect of protein-protein interactions (PPI) is fundamental to gain insight into the complex signaling system of a human cell. A plethora of methods has been suggested to infer PPI from data on a large scale, but none of them is able to characterize the effect of this interaction. Here, we present a novel computational development that employs mitoti...

Detection of protein-protein interactions (PPIs) is important for understanding numerous processes in mammalian cells; however, existing PPI detection methods often give significant background signals. Here, we propose a novel PPI-detection method based on kinase-mediated growth induction of mammalian cells. In this method, target proteins are fused to the intracellular domain of c-kit (c-kit I...

Protein-protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction information Extraction system) is a configurable...

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evol...

Protein-protein interactions (PPI) are involved in a myriad of cellular processes, and their deregulation can lead to many diseases. One such process is protein ubiquitination that requires an orchestrated action three key enzymes add ubiquitin moieties substrate proteins. Importantly, this reversible through deubiquitinating enzymes. Both deubiquitination require PPIs once classified be utiliz...

The Hippo signal transduction cascade controls cell growth, proliferation and death, all of which are frequently deregulated in tumour cells. Since initial studies in Drosophila melanogaster were instrumental in defining Hippo signalling, the machinery was named after the central Ste20-like kinase Hippo. Moreover, given that loss of Hippo signalling components Hippo, Warts, and Mats resulted in...

Inhibiting protein-protein interactions (PPIs) with synthetic molecules remains a frontier of chemical biology. Many PPIs have been successfully targeted by mimicking α-helices at interfaces, but most PPIs are mediated by nonhelical, nonstrand peptide loops. We sought to comprehensively identify and analyze these loop-mediated PPIs by writing and implementing LoopFinder, a customizable program ...

Protein–protein interactions (PPIs) are implicated in almost all biological processes for any given protein engaged in complexes with other proteins for themajority of its lifetime. In this regard, proteins function not merely as single, isolated entities, but display their roles by interacting with other cellular components. The different interaction patterns are at least as important as the i...

Association and dissociation of protein molecules are crucial for most of the cellular processes. A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Analysis and classification of PPIs may help to recognize certain interface binding organizations shared by different protein families, which may be importan...