MOTIVATION Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-p...

Following recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections reve...

The ubiquitin-proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome-the protease responsible for the degradation of ubiquitylated proteins-several structural and functional questions remain unanswered. To gain more insight into the assembly and function of the metazoan 26S proteasome, a two-hybrid...

Summary: The construction of genome wide protein–protein interaction maps makes it feasible to study the global organization of proteins in a biological cell. Here the module organization of the protein–protein interaction network (PPIN) of budding yeast are investigated by Netwalk, an algorithm based on biased random (Brownian) walks. The yeast PPIN is a highly modular network, it has a modula...

The growth of neuronal processes depends critically on the function of adhesion proteins that link extracellular ligands to the cytoskeleton. The neuronal adhesion protein L1-CAM serves as a receptor for nerve growth-promoting proteins, a process that is inhibited by the interaction between L1-CAM and the cytoskeleton adaptor ankyrin. Using a novel reporter based on intramolecular bioluminescen...

Protein Interaction VisualizatiOn Tool (PIVOT) is a visualization tool for protein-protein interactions. It allows the user to create personal data sets of interactions by combining information from private and public data sources. The user can gradually access the interactions' data using a clear interactive map that is focused on the researcher's protein of interest, and is reshaped and expan...

Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with complementary datasets of protein function and int...

Human Leukocyte Antigen (HLA) complexes are critical cell-surface protein assemblies that facilitate T-cell surveillance of almost all cell types in the body. While receptor binding to HLA class I and II is well-described with detailed structural information, nature cis interactions within plasma membrane surveyed cells remains be better characterized, as protein-protein environment technically...

background: fragile histidine triad protein (fhit), as a known tumor suppressor protein, has been proposed to play crucial role in inhibiting p53 degradation by mdm2. studies have confirmed fhit interaction with p53 or mdm2, although functional interacting domains of fhit with mdm2 and/or p53 are not completely defined. thus, through determining the significant structural interacting domains of...

The protein-ligand interacting mechanism is essential to biological processes and drug discovery. The SiMMap server statistically derives site-moiety map with several anchors, which describe the relationship between the moiety preferences and physico-chemical properties of the binding site, from the interaction profiles between query target protein and its docked (or co-crystallized) compounds....