The intracellular metabolic fluxes can be calculated by metabolic flux analysis, which uses a stoichiometric model for the intracellular reactions along with mass balances around the intracellular metabolites. In this study, we have constructed in silico metabolic pathway network of Escherichia coli consisting of 301 reactions and 294 metabolites. Metabolic flux analyses were carried out to est...

Many important processes affecting the earth’s climate are determined by physical properties of seawater. In addition, desalination seawater is a significant source drinking water for human population living in coastal areas. Since governing these depend on molecular interactions among its components, deeper knowledge at level would contribute to better understanding phenomena. However, strong ...

In pharmaceutical industry ligand based approaches like scaffold hopping, scaffold decoration and me-too approaches, are used to generate lead structures in discovery projects. We use several tools to generate novel lead structures, such as BROOD [1]. BROOD is a software tool which explores chemical space around query molecules based on shape similarity and electrostatics, and it generates anal...

In this study, an in silico genome-scale metabolic model of steroidogenesis was used to investigate the effects of hypoxic stress on steroid hormone productions in fish. Adult female fathead minnows (Pimephales promelas) were exposed to hypoxia for 7 days with fish sub-sampled on days 1, 3 and 7 of exposure. At each time point, selected steroid enzyme gene expressions and steroid hormone produc...

The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in silico screening procedure which was focused on finding novel, EPHA4 hinge binding fragments. This...

Wound and bone fracture healing are natural repair processes initiated by trauma. Over the last decade, many mathematical models have been established to investigate the healing processes in silico, in addition to ongoing experimental work. In recent days, the focus of the mathematical models has shifted from simulation of the healing process towards simulation of the impaired healing process a...