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...

Academic researchers and many in industry often lack the financial resources available to scientists working in "big pharma." High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screeni...

Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively paral...

SFI WORKING PAPER: 2014-04-006 SFI Working Papers contain accounts of scientific work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in peer-reviewed journals or proceedings volumes, but not papers that have already appeared in print. Except for papers by our external faculty, papers must be based on work done at ...

cancer is one of the causes of death in the world. several treatment methods exist against cancer cells such as radiotherapy and chemotherapy. since traditional methods have side effects on normal cells and are expensive, identification and developing a new method to cancer therapy is very important. antimicrobial peptides, present in a wide variety of organisms, such as plants, amphibians and ...

Enteropathogenic E. coli (EPEC) is a human pathogen using type III secretion system for delivery of proteins directly into the human host. The system contains a single ATPase, EscN, which is essential for uncoupling of proteins from their complexes with chaperones before the delivery. The structure of EscN ATPase (PDB code: 2obm) was used to construct a search template to screen computationally...

similarities to glandular carcinoma. On the other hand, dysregulation of the in silico principle governing proliferation had muted effects on growth morphologies. Comparatively, the 2 alterations and their misbalance gave rise to distinct morphologies that mark intermediate stages of a simulated progression toward malignancy. In cases where unchecked growth was observed, we identified structura...

introduction: influenza a virus causes unpredictable epidemics and pandemics by creating antigenic variations. with the appearance of each new strain, rapid emergency countermeasures are taken against this new strain. hence, designing an applicable and cross protective strategy to counter this virus is of great importance. to achieve this, choosing conserved antigenic regions in influenza virus...