Sequence patches on MAPK surfaces define protein-protein interactions

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

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...

Discovering Domains Mediating Protein Interactions

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 in...

Protein-protein interactions define specificity in signal transduction.

Virtually every aspect of cellular function within a metazoan organism, including proliferative status, metabolism, gene expression, cytoskeletal organization, and indeed the cell’s very survival, is dependent on external signaling molecules, either in the form of soluble hormones or proteins anchored to the surface of an adjacent cell or the extracellular matrix (ECM). These factors exert thei...

Protein-lipid interactions on the surfaces of cell membranes.

Simple sequence-based kernels do not predict protein-protein interactions

MOTIVATION A number of methods have been reported that predict protein-protein interactions (PPIs) with high accuracy using only simple sequence-based features such as amino acid 3mer content. This is surprising, given that many protein interactions have high specificity that depends on detailed atomic recognition between physiochemically complementary surfaces. Are the reported high accuracies...