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Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to identify complexes from the protein interaction (PPI) networks of individual species, these are severely limited by noise and errors (false positives) in currently available datasets. Our analysis using human and yeast PPI networks revealed that these methods missed several important complexes including those conserved between the two species (e.g. the MLH1-MSH2-PMS2-PCNA mismatch-repair complex). Here, we note that much of the functionalities of yeast complexes have been conserved in human complexes not only through sequence conservation of proteins but also of critical functional domains. Therefore, integrating information of domain conservation might throw further light on conservation patterns between yeast and human complexes.
The recognition of essential proteins not only can help to understand the mechanism of cell operation, but also help to study the mechanism of biological evolution. At present, many scholars have been discovering essential proteins according to the t
Are turn-on and turn-off functions in protein-protein interaction networks exact opposites of each other? To answer this question, we implement a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutati
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a network t
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contai
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in