Protein complexes play an important role in cellular mechanism. Identification of protein complexes in protein-protein interaction (PPI) networks is the first step in understanding the organization and dynamics of cell function. Several high-throughput experimental techniques produce a large amount of protein interactions, which can be used to predict protein complexes in a PPI network. We have...

We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature. This method outperforms previously developed PPI prediction algorithms that rely on the conjunction of two protein names in MEDLINE abstracts. We show significant increases in coverage (76% versus 32%) and sensitivity (66% versus 41% at a sp...

MOTIVATION Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the en...

Background and objectives: Non-alcoholic fatty liver disease (NAFLD) is a common liver condition. On the other hand, coffee consumption has shown promising for gastrointestinal diseases.  Detection of the most valuable biomarkers of decaffeinated coffee treatment in healthy and non-alcoholic fatty liver disease conditions was the aim of the present study. Methods:</stro...

Clustering protein-protein interaction (PPI) network data yields groups of proteins that are biochemically involved. Most existing clustering methods treat all the proteins in a PPI network equally. However, analyzing host-pathogen networks requires identification of clusters that represent the interactions between the set of pathogen proteins and the set of host proteins. For studying HIV-huma...

Relations between entities in text have been widely researched in the natural language processing and informationextraction communities. The region connecting a pair of entities (in a parsed sentence) is often used to construct kernels or feature vectors that can recognize and extract interesting relations. Such regions are useful, but they can also incorporate unnecessary distracting informati...

Protein-protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction information Extraction system) is a configurable...

The detection and analysis of protein complexes is essential for understanding the functional mechanism cellular integrity. Recently, several techniques detecting analysing from Protein–Protein Interaction (PPI) dataset have been developed. Most those are inefficient in terms detecting, overlapping complexes, exclusion attachment complex core, inability to detect inherent structures underlying ...

objective(s): first, 10-bromodecanoic acid was covalently attached to all available surface primary amines of ppi g2 and g3 to increase their lipophilicity. in the subsequent step, ppis were conjugated to the alkylcarboxylate groups of alkylcarboxylate-ppi derivatives to increase the number of surface primary amines. physicochemical properties of modified ppis were determined. transfection expe...