Chemical cross-linking (CX) of proteins in vivo or cell free extracts followed by mass spectrometric (MS) identification linked peptide pairs (CXMS) can reveal protein-protein interactions (PPIs) both at a proteome wide scale and the level cross-linked amino acid residues. However, error estimation PPI remains challenging large datasets. Here we discuss recent advances recognition spurious inte...

Protein isolate is used in the food industry in order to process and stabilise food foams. Thereforethere has been a great deal of interest and research in order to understand the effect of processingparameters on the functional properties of the isolate. The major purpose of this research is to studythe foamability of the different proteins - starch nano-particle system. The results from exper...

The overall goal is to establish a reliable human protein-protein interaction network and develop computational tools to characterize a protein-protein interaction (PPI) network and the role of individual proteins in the context of the network topology and their expression status. A novel and unique feature of our approach is that we assigned confidence measure to each derived interacting pair ...

Protein-protein complexes play key roles in all cellular signal transduction processes. We have developed a fast and accurate computational approach to predict changes in the binding free energy upon alanine mutations in protein-protein interfaces. The approach is based on a knowledge-based scoring function, DrugScore(PPI), for which pair potentials were derived from 851 complex structures and ...

conclusions our results revealed the possible crucial genes and mirnas involved in the initiation and progression of hcc cells infected with hcv. results based on the topological analysis of mirna-hubgene network, we identified the key hub mirnas. in order to identify the most important common sub-network, we aligned two ppi networks using netal tool. the c-jun gene was identified as the most i...

Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) pat...

It has been claimed that protein-protein interaction (PPI) networks are scale-free, and that identifying high-degree "hub" proteins reveals important features of PPI networks. In this paper, we evaluate the claims that PPI node degree sequences follow a power law, a necessary condition for networks to be scale-free. We provide two PPI network examples which clearly do not have power laws when a...

Motivations Protein interaction databases archive proteinprotein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate “the interactome”. We have developed mentha, a new resource that addresses this problem. mentha archives evidence about PPI in the human proteome evidence collected from d...

Protein phosphorylation is a reversible post-translational modification where a protein kinase adds a phosphate group to a protein, potentially regulating its function, localization and/or activity. Phosphorylation can affect protein-protein interactions (PPIs), abolishing interaction with previous binding partners or enabling new interactions. Extracting phosphorylation information coupled wit...

Detection of protein-protein interactions (PPIs) is important for understanding numerous processes in mammalian cells; however, existing PPI detection methods often give significant background signals. Here, we propose a novel PPI-detection method based on kinase-mediated growth induction of mammalian cells. In this method, target proteins are fused to the intracellular domain of c-kit (c-kit I...