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Automated webserver and some downloadable programs. RaptorX. remote homology detection, protein 3D modeling, binding site prediction. Automated webserver and Downloadable program. Biskit. wraps external programs into automated workflow. BLAST search, T-Coffee alignment, and MODELLER construction. ESyPred3D.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease.
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the " target " protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the " template "). Homology modeling relies on the identification of one or more known protein ...
iBioSim [5] [6] is a computer-aided design (CAD) tool for the modeling, analysis, and design of genetic circuits. GUI/Scripting tool [7] for building and simulating multicellular models. Yes, but only for reactions. GUI tool [8] [9] for analyzing and simulating SBML models.
Serial passage is the process of growing bacteria or a virus in iterations. For instance, a virus may be grown in one environment, and then a portion of that virus population can be removed and put into a new environment. This process is repeated with as many stages as desired, and then the final product is studied, often in comparison with the ...
A program to predict lowest free energy structures and base pair probabilities for RNA or DNA sequences. Programs are also available to predict maximum expected accuracy structures and these can include pseudoknots. Structure prediction can be constrained using experimental data, including SHAPE, enzymatic cleavage, and chemical modification ...
Infectious disease dynamics. Mathematical models need to integrate the increasing volume of data being generated on host - pathogen interactions. Many theoretical studies of the population dynamics, structure and evolution of infectious diseases of plants and animals, including humans, are concerned with this problem.
SEA-PHAGES is a two-semester undergraduate research program administered by the University of Pittsburgh's Graham Hatfull 's group and the Howard Hughes Medical Institute's Science Education Division. Students from over 100 universities nationwide engage in authentic individual research that includes a wet-bench laboratory and a bioinformatics ...