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Networks are employed to represent many real world complex systems. For biological systems, biomolecules interact with each other to form so-called biomolecular networks. The explorations on the connections between structural control theory and biological networks have uncovered some interesting biological phenomena. Recently, some studies have paid attentions to the structural controllability of...
Diabetes Mellitus Type 2 is one of the common diseases and found worldwide. The cause of this abnormality is due to lack of insulin production. Glucagon like peptide-1 (GLP-1), product of the glucagon gene is one of the prime components which stimulates the β cell proliferation and inhibits β cell death. DiPeptidyl Peptidase IV (DPP IV) acts as protease degrading incretins which stimulates the secretion...
Traditionally, most researches in development of new drug target focus on relationship between a target protein and a related compound by experimental or computational approaches. In addition to the translational level, it is useful tool control disease at the transcriptional level, if we identify transcription factors that regulate expression of target proteins. We introduce new methodology that...
It is well established that oxidative stress (OS) plays a major role in male infertility. OS occurs when the production of potentially destructive reactive oxygen species (ROS) exceeds the body's own natural antioxidant defenses, resulting in cellular damage. Antioxidant and trace element supplementation to infertile men has shown considerable improvement in sperm parameters; however, the issue of...
Identifying possible viral-host protein-protein interactions is an important and useful approach in developing new drugs targeting those interactions. In this article, a recently published dataset containing records of interactions between a set of HIV-1 proteins and a set of human proteins has been analyzed using association rule mining. The main objective is to identify a set of association rules...
Abstract-Prediction of protein-proteininteraction sites is very important to the function of a protein and drug design. In this paper, we adequately utilize the characters of ensemble learning, which can improve the accuracy of individual classifier and generalization ability of the system, and propose a new prediction method of protein-protein interaction sites: ensemble learning method based on...
Removal or suppression of key proteins in an essential pathway of a pathogen is expected to disrupt the pathway and prohibit the pathogen from performing a vital function. Thus disconnecting multiple essential pathways should disrupt the survival of a pathogen even when it has multiple pathways to drug resistance. We consider a scenario where the drug-resistance pathways are unknown. To disrupt these...
Following the availability of whole genome sequence of Mycobacterium tuberculosis (MTB) in public database, the anticipation of its benefits would definitely falls into the contribution towards development of improved vaccine or drug discovery to fight against the fatal disease, tuberculosis (TB). This research aimed to scan the whole genome sequence of MTB by application of bioinformatics approaches...
The tumor suppressor protein, p53, and its downstream effectors play a central role in mediating process of cellular repair or cell death in response to a wide variety of cellular stress. Cell fate varies, depending on the type of stress, its level and the genetic background of individual cell types. By using quantitative time-lapse microscopy to track dynamics of individual cells in real time, we...
Despite intense investment growth and technology development, there is an observed bottleneck in drug discovery and development over the past decade. NIH started the Molecular Libraries Initiative (MLI) in 2004 to enlarge the pool for potential drug targets, especially from the “undruggable” part of human genome, and potential drug candidates from much broader types of drug-like small molecules. In...
WISDOM is an international initiative to deploy large-scale in-silico docking on a public grid infrastructure in an attempt to find potential drugs against neglected or emerging diseases such as Malaria and Avian Flu. Within the framework of the WISDOM initiative, large-scale deployments of in silico docking have been done on production grid infrastructures, demonstrating the relevance of large scale...
Application of atomic force microscopy (AFM) in liquid is necessary for imaging and manipulation of biological specimens. The atomic force microscope (AFM) has become an indispensable tool in biology because it permits the imaging and probing of nanomechanical properties of biological samples such as biopolymers and viruses under physiological (liquid environments) conditions. In this paper, we have...
This paper presents a mathematical model for a novel synthetic gene regulatory network. The aim of this circuit is to behave as a bistable switch for in vivo delivery of short hairpin RNA (shRNA) which can induce RNA interference (RNAi) of a target mRNA. Through the mathematical analysis performed here, it will be shown how the circuit can be controlled to induce sustained expression of a shRNA, with...
The identification of protein-protein interface residues is essential for drug design, understanding cell activity of organism. In this paper, a couple of covering algorithms are presented to predict protein-protein interaction sites by using several protein features, such as sequence profile, residue entropy and so on. These features are utilized to construct covering algorithms classifiers to identify...
AutoDock is a widely used automated protein docking program in structure-based drug-design. Different search algorithms such as simulated annealing, traditional genetic algorithm (GA) and Lamarckian genetic algorithm (LGA) are implemented in AutoDock. However, the docking performance of these algorithms is still limited by the local optima issue of simulated annealing or the premature convergence...
The item-level traceability is a very important requirement for many practical application scenarios, where it needs to guarantee perfect transparency for products flow along the whole supply chain. Among these, the pharmaceutical distribution is a very interesting scenario, characterized by many challenges, where, the Radio Frequency Identification (RFID) technology will play a very important role...
The purpose of this article was to observe interaction between drug and cancer cell with fluorescence probes and molecular imaging technology. In order to study the effect of cell growth and apoptosis morphology of Human gastric adenocarcinoma SGC-7901 induced by n-butanol extract from Capparis spionosa L. (CSBE), laser scanning microscopy was employed to observe apoptosis imaging. In addition, the...
The purpose of this article was to observe interaction between drug and cancer cell with fluorescence probes and molecular imaging technology. In order to study the effect of cell growth and apoptosis morphology of Human gastric adenocarcinoma SGC-7901 induced by n-butanol extract from Capparis spionosa L. (CSBE), laser scanning microscopy was employed to observe apoptosis imaging. In addition, the...
Computational structure prediction, including de novo and homology modeling, is an important tool for membrane protein studies. Developing an accurate scoring function that can be used for structure discrimination and assessment remains a challenge. In our previous work, we have analyzed a set of high-resolution membrane protein structures using the network approach developed in our lab and proposed...
Nrf-2(Nuclear factor erythroid 2-related factor 2)/HO-1(Heme Oxygenase-1) signaling pathway plays an important role in the suppression of carcinoma, The study aims to investigate the effect of Curcumin on the expression of HO-1 and Nrf-2, which will provide a therapeutic intervention for treatment of carcinoma. SHSY5Y cells were treated with Curcumin at 0, 1.25, 5.0, 20.0 μM for the time course assay...
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