Molecular function in cellular processes is governed by protein-protein interactions (PPIs) within biological networks. Selective yet specific association of these protein partners contributes to diverse functionality such as catalysis, regulation, assembly, immunity, and inhibition in a cell. Therefore, understanding the principles of protein-protein association has been of immense interest fo...

Protein phosphorylation is a central regulatory mechanism in signal transduction involved in most biological processes. Phosphorylation of a protein may lead to activation or repression of its activity, alternative subcellular location and interaction with different binding partners. Extracting this type of information from scientific literature is critical for connecting phosphorylated protein...

Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein-protein interactions (PPIs) among closely related species and their hybrids. We examine in vivo ...

The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one's attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide intera...

Comprehensive approaches to detect protein-protein interactions (PPIs) have been most successful in the yeast model system. Here we present "Cross-and-Capture," a novel assay for rapid, sensitive assessment of PPIs via pulldown of differently tagged yeast strain arrays. About 500 yeast genes that function in DNA replication, repair, and recombination and nuclear proteins of unknown function wer...

Previous mechanistic studies have suggested a possible interaction between proton pump inhibitor (PPIs) and clopidogrel. However, the results of clinical trials about the effects of PPIs on safety and efficacy of clopidogrel are controversial. The study sought to estimate the impact of PPIs on antiplatelet effect of clopidogrel. The study performed a meta-analysis of comparative concomitant use...

The majority of gene products that crowd a living cell interact, at least transiently, with other protein molecules. Concordantly, virtually all cellular events are mediated by protein-protein interactions (PPIs). The same applies to host-pathogen systems, where PPIs are essential in host colonization and infection. Some authors believe that the understanding of the human interactome will provi...

Protein-protein interactions (PPIs) play various important roles in living organisms. Hence, many efforts have been made to investigate and predict PPIs. Analysis of strengths of PPIs is important as well as PPIs because such strengths are involved in functionality of proteins. In this paper, we propose several feature space mappings from protein pairs, which make use of protein domain informat...

Proton pump inhibitors (PPIs) have been recommended for reducing the risk of gastrointestinal bleeding associated with dual antiplatelet therapy (aspirin plus clopidogrel). However, studies have found decreased efficacy of clopidogrel when concurrently administered with a PPI. To determine the mechanism of and evidence for the potential interaction between clopidogrel and PPIs, along with the c...

MOTIVATION Protein-protein interactions (PPIs), though extremely valuable towards a better understanding of protein functions and cellular processes, do not provide any direct information about the regions/domains within the proteins that mediate the interaction. Most often, it is only a fraction of a protein that directly interacts with its biological partners. Thus, understanding interaction ...