Protein-protein interactions (PPIs) are frequently mediated by the binding of a modular domain in one protein to a short, linear peptide motif in its partner. The advent of proteomic methods such as peptide and protein arrays has led to the accumulation of a wealth of interaction data for modular interaction domains. Although several computational programs have been developed to predict modular...

Most of a cell’s functional processes involve interactions among proteins, and a key challenge in proteomics is to better understand these complex interaction graphs at a systems level. Because of their importance in development and disease, protein-protein interactions (PPIs) have been the subject of intense research in recent years. In addition, a greater understanding of PPIs can be achieved...

background: protein-protein interactions do not provide any direct information re­garding the domains within the proteins that mediate the interactions. the majority of proteins are multi domain proteins and the interaction between them is often defined by the pairs of their domains. most of the former studies focus only on interacting do­main pairs. however they do not consider the interaction...

Protein-protein interactions (PPIs) are of central importance for many areas of biological research. Several complementary high-throughput technologies have been developed to study PPIs. The wealth of information that emerged from these technologies led to the first maps of the protein interactomes of several model organisms. Many changes can occur in protein complexes as a result of genetic an...

In this review, we discuss the structural and functional diversity of protein-protein interactions (PPIs) based primarily on protein families for which three-dimensional structural data are available. PPIs play diverse roles in biology and differ based on the composition, affinity and whether the association is permanent or transient. In vivo, the protomer's localization, concentration and loca...

Protein-protein interaction (PPI) maps provide insight into cellular biology and have received considerable attention in the post-genomic era. While large-scale experimental approaches have generated large collections of experimentally determined PPIs, technical limitations preclude certain PPIs from detection. Recently, we demonstrated that yeast PPIs can be computationally predicted using re-...

Protein-protein interactions (PPIs) mediate the transmission and regulation of oncogenic signals that are essential to cellular proliferation and survival, and thus represent potential targets for anti-cancer therapeutic discovery. Despite their significance, there is no method to experimentally disrupt and interrogate the essentiality of individual endogenous PPIs. The ability to computational...

Motivation: Many methods predict the physical interaction between two proteins (protein-protein interactions; PPIs) from sequence alone. Their performance drops substantially for proteins not used for training. Results: Here, we introduce a new approach to predict PPIs from sequence alone which is based on evolutionary profiles and profile-kernel support vector machines. It improved over the st...

Increasing demand for the knowledge about protein-protein interactions (PPIs) is promoting the development of methods for predicting protein interaction network. Although high-throughput technologies have generated considerable PPIs data for various organisms, it has inevitable drawbacks such as high cost, time consumption, and inherently high false positive rate. For this reason, computational...

Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforwar...