Motivation: Protein–protein interactions (PPIs) underpin virtually all cellular processes both in health and disease. Modulating the interaction between proteins by means of small (chemical) agents is therefore a promising route for future novel therapeutic interventions. In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs. Results: We reported a novel c...

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...

BACKGROUND In the last decade, the inhibition of protein-protein interactions (PPIs) has emerged from both academic and private research as a new way to modulate the activity of proteins. Inhibitors of these original interactions are certainly the next generation of highly innovative drugs that will reach the market in the next decade. However, in silico design of such compounds still remains c...

Although mass spectrometry has been frequently used to identify proteins, there are no web servers that provide comprehensive functional annotation of those identified proteins. It is necessary to provide such web service due to a rapid increase in the data. We, therefore, introduce MassNet, which provides (i) physico-chemical analysis information, (ii) KEGG pathway assignment (iii) Gene Ontolo...

The E3 ubiquitin protein ligase Casitas B-lineage Lymphoma (Cbl) proteins and their binding partners play an important role in regulating signal transduction pathways. It is important to utilize regulators to study the protein-protein interactions (PPIs) between these proteins. However, finding specific small-molecule regulators of PPIs remains a significant challenge due to the fact that the i...

The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein-protein interactions ...

MOTIVATION Protein-protein interactions (PPIs) underpin virtually all cellular processes both in health and disease. Modulating the interaction between proteins by means of small (chemical) agents is therefore a promising route for future novel therapeutic interventions. In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs. RESULTS We reported a novel c...

MOTIVATION Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein-protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows P...

Membrane receptor-sensed input signals affect and modulate intracellular protein-protein interactions (PPIs). Consequent changes occur to the compositions of protein complexes, protein localization and intermolecular binding affinities. Alterations of compartmentalized PPIs emanating from certain deregulated kinases are implicated in the manifestation of diseases such as cancer. Here we describ...

Cellular signal transduction is a complex process involving protein-protein interactions (PPIs) that transmit information. For example, signals from the plasma membrane may be transduced to transcription factors to regulate gene expression. To obtain a global view of cellular signaling and to predict potential signal modulators, we searched for protein interaction partners of more than 450 sign...