For the two SH3 domains, BOI1 and BOI2, the prediction was almost random. The low sequence homology of the template structures might have caused the failure in the homology modeling. Therefore, application of our methods to the domains whose structures cannot be reliably predicted would be inappropriate. In this study, we developed several methods to improve binding energy calculation and they showed promising results. However, the overall performance was not sufficient to accurately predict the binding specificity of many SH3 domains. For three blind tested SH3 domains in DREAM4, our method could not predict the general pattern of binding peptides in one case. This calls further research on the binding energy calculation. Our method also requires a large number of computations due to the conformation sampling process with MD simulation. Moreover the sampled conformations are highly dependent on the sequences of the peptides. Thus, development of more efficient and general conformation sampling methods would be required to improve computational binding energy prediction. When yeast cells are grown to a high density, starved for a short period, and then continuously fed low concentrations of glucose using a chemostat, the cell population becomes highly synchronized and undergoes robust oscillations in oxygen consumption termed yeast metabolic cycles. Such cycles can range anywhere from 40 minutes to over 10 hours depending on the continuous glucose concentration. They consist of phases of rapid oxygen consumption that alternate with phases of minimal oxygen consumption. A variety of growth and metabolic parameters such as budding index, storage carbohydrate content, PF-4217903 ethanol levels, and carbon dioxide production have been observed to oscillate as a function of such cycles, although not necessarily in phase with the dissolved oxygen oscillation. The OX phase represents the peak of mitochondrial respiration and is associated with a rapid induction of ribosomal genes and other genes involved in growth. Cell division and the upregulation of genes that encode mitochondrial proteins occur during the RB phase, when the rate of oxygen consumption begins to decrease. In the RC phase, many genes associated with stress and starvation-associated responses are activated prior to the next OX phase. Studies of these cycles have revealed the changes in metabolism that occur during the life of a yeast cell and provided significant insight into how a number of important cellular processes might be coordinated with metabolism. However, it is not known whether such metabolic cycles might occur in single individual cells in the wild, in the absence of a glucose-limited, steady-state growth environment maintained by the chemostat. Moreover, in each permissive window of the YMC, approximately half of the cell population initiates the cell division process, raising questions about the metabolic.