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Simulation of Biological Processes phần 5

Ở đây tôi sẽ trình bày một quan điểm tiến hóa về chủ đề này phức tạp. Thay vì thảo luận Monte Carlo phương pháp, các mô hình đại lý dựa trên, hệ thống hạt tương tác, và ngẫu nhiên và | FIG. 4. KEGG pathway diagram for lysine biosynthesis. THE KEGG DATABASE 99 The KEGG Reference Network Matching genes in the genome against gene products in the network Gene products in the pathway or complex Ortholog identifiers Extension of EC numbers FIG. 5. KEGG reference network for knowledge-based prediction. Genes in the genome native network are computable which is like computing small perturbations around the native structure of a protein. However the dynamics of cell differentiation for example would be extremely difficult to compute which is like computing the dynamics of protein folding from the extended chain to the native structure. A perturbation to the network may be internal or external. An internal perturbation is a genomic change such as a gene mutation or a molecular change such as a protein modification and an external perturbation is a change in the environment of the cell. Although we do not yet have a proper way to compute dynamic responses of the network to small perturbations a general consideration can be made. Figure 7 illustrates the basic system architecture that results from the interactions with the environment. The basic principle of the native structure formation of a globular protein is that it consists of the conserved hydrophobic core to stabilize the globule and the divergent hydrophilic surface to perform specific functions. The protein interaction network in the cell seems to have a similar dual architecture. It consists of the conserved core such as metabolism for the basic maintenance of life and the divergent surface such as transporters and receptors for interactions with the environment. The subnetwork of genetic information processing may also have a dual architecture the conserved core of RNA polymerase and ribosome and the divergent surface of transcription factors. In both cases the core is encoded by a set of orthologous genes that are conserved among organisms and the surface is 100 KANEHISA 1. Generate networks by