Many proteins are known to perform their own functions when they form particular groups of proteins, called protein complexes. With the advent of large-scale protein-protein interaction (PPI) studies, it has been a challenging problem in systems biology to predict protein complexes from PPIs. In this paper, we propose a novel method, called Repeated Simulated Annealing of Partitions of Proteins...

MOTIVATION Protein-protein interaction (PPI) extraction from published biological articles has attracted much attention because of the importance of protein interactions in biological processes. Despite significant progress, mining PPIs from literatures still rely heavily on time- and resource-consuming manual annotations. RESULTS In this study, we developed a novel methodology based on Bayes...

Protein-protein interactions (PPIs), involved in many biological processes such as cellular signaling, are ultimately encoded in the genome. Solving the problem of predicting protein interactions from the genome sequence will lead to increased understanding of complex networks, evolution and human disease. We can learn the relationship between genomes and networks by focusing on an easily appro...

Inhibiting protein-protein interactions (PPIs) with synthetic molecules remains a frontier of chemical biology. Many PPIs have been successfully targeted by mimicking α-helices at interfaces, but most PPIs are mediated by nonhelical, nonstrand peptide loops. We sought to comprehensively identify and analyze these loop-mediated PPIs by writing and implementing LoopFinder, a customizable program ...

aim: this study is aimed to elicit the possible correlation between breast and colon cancer from molecular prospectiveby analyzing and comparing pathway-based biomarkers.background: breast and colon cancer are known to be frequent causes of morbidity and mortality in men and womenaround the world. there is some evidence that while the incident of breast cancer in young women is high, it is repo...

Background: Prediction of the protein localization is among the most important issues in the bioinformatics that is used for the prediction of the proteins in the cells and organelles such as mitochondria. In this study, several machine learning algorithms are applied for the prediction of the intracellular protein locations. These algorithms use the features extracted from pro...

Protein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist da...

Association and dissociation of protein molecules are crucial for most of the cellular processes. A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Analysis and classification of PPIs may help to recognize certain interface binding organizations shared by different protein families, which may be importan...

Essentially all biological processes depend on protein-protein interactions (PPIs). Timing of such interactions is crucial for regulatory function. Although circadian (~24-hour) clocks constitute fundamental cellular timing mechanisms regulating important physiological processes, PPI dynamics on this timescale are largely unknown. Here, we identified 109 novel PPIs among circadian clock protein...