Research papers
2003 · Analytical Chemistry · 5,011 citations
A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample. Peptides that correspond to more than a single protein in the sequence database are apportioned among all corresponding proteins, and a minimal protein list sufficient to account for the observed peptide assignments is derived using the expectation-maximization algorithm. Using peptide assignments to spectra generated from a sample of 18 purified proteins, as well as complex H. influenzae and Halobacterium samples, the model is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications. This method allows filtering of large-scale proteomics data sets with predictable sensitivity and false positive identification error rates. Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments.
2012 · Journal of Chemical Information and Modeling · 2,589 citations
ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org.
2017 · Journal of Oncological Sciences · 306 citations
Cancer is a disease at the cellular level involving heritable disorders in cellular control mechanism. Cancer cells also need to adapt their metabolism to survive and multiply under the metabolically compromised conditions provided by the tumor microenvironment. Tumor cells alter their metabolism to maintain unregulated cellular proliferation and survival, but this transformation leaves them reliant on constant supply of nutrients and energy. They alter their metabolism to support their rapid proliferation and expansion across the body. After the discovery of based on the altered cancer cell metabolism in 1930, loads of studies have shed light on several aspects of cancer metabolism with a common goal to find new ways for effectively eliminating tumor cells by targeting their energy metabolism. Research has directed most of its resources to elucidate the causes, prevention and possible cure for cancer, yet the process has been elusive claiming human lives more than ever. This disease is a manifestation of etiological and pathological disturbances of mechanisms that control cell division, differentiation and metabolism. 50% of all human tumors carry genetic alterations that lead to the inactivation of some tumor suppressor proteins. Cancer cells are shown to experience characteristic changes in their metabolic programs, including increased uptake of glucose, enhanced rates of glutaminolysis and fatty acids synthesis, suggesting that metabolic shifts supports tumor cells growth and survival. In this review, we summarized the major concepts of glucose metabolization and explore the molecular basis of aerobic glycolysis of cancer cells.