Guang Qiang Dong

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Applications in structural biology and medicinal chemistry require protein-ligand scoring functions for two distinct tasks: (i) ranking different poses of a small molecule in a protein binding site and (ii) ranking different small molecules by their complementarity to a protein site. Using probability theory, we developed two atomic distance-dependent(More)
One aim of synthetic biology is to exert systematic control over cellular behavior, either for medical purposes or to "program" microorganisms. An engineering approach to the design of biological controllers demands a quantitative understanding of the dynamics of both the system to be controlled and the controllers themselves. Here we focus on a widely used(More)
Enzymes in the glutathione transferase (GST) superfamily catalyze the conjugation of glutathione (GSH) to electrophilic substrates. As a consequence they are involved in a number of key biological processes, including protection of cells against chemical damage, steroid and prostaglandin biosynthesis, tyrosine catabolism, and cell apoptosis. Although(More)
MOTIVATION Statistical potentials have been widely used for modeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between proteins, nucleic acids and small molecules. Here, we formulate the statistical potentials entirely within a statistical framework, avoiding questionable statistical mechanical assumptions and(More)
Fluorescent proteins are frequently used as reporters for gene expression in living cells, either by being expressed in tandem with a protein of interest or through the creation of fusion proteins. The data yielded by the fluorescence output are of considerable interest in efforts to formulate quantitative models of cellular behavior underway in fields such(More)
Biological systems often involve chemical reactions occurring in low-molecule-number regimes, where fluctuations are not negligible and thus stochastic models are required to capture the system behaviour. The resulting models are generally quite large and complex, involving many reactions and species. For clarity and computational tractability, it is(More)
Simulating the major molecular events inside an Escherichia coli cell can lead to a very large number of reactions that compose its overall behaviour. Not only should the model be accurate, but it is imperative for the experimenter to create an efficient model to obtain the results in a timely fashion. Here, we show that for many parameter regimes, the(More)
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