Analysis of Oncogene Protein Structure Using Small World Network Concept

Prediction of Metal Ion Binding Sites of Transmembrane Proteins

The metal ion binding of transmembrane proteins (TMPs) plays a fundamental role in biological processes, pharmaceutics, and medicine, but it is hard to extract enough TMP structures in experimental techniques to discover their binding mechanism comprehensively. To predict the metal ion binding sites for TMPs on a large scale, we present a simple and effective two-stage prediction method TMP-MIBS, to identify the corresponding binding residues using TMP sequences. At present, there is no specific research on the metal ion binding prediction of TMPs. Thereby, we compared our model with the published tools which do not distinguish TMPs from water-soluble proteins. The results in the independent verification dataset show that TMP-MIBS has superior performance. This paper explores the interaction mechanism between TMPs and metal ions, which is helpful to understand the structure and function of TMPs and is of great significance to further construct transport mechanisms and identify potential drug targets.

Application of Multilayer Network Models in Bioinformatics

Multilayer networks provide an efficient tool for studying complex systems, and with current, dramatic development of bioinformatics tools and accumulation of data, researchers have applied network concepts to all aspects of research problems in the field of biology. Addressing the combination of multilayer networks and bioinformatics, through summarizing the applications of multilayer network models in bioinformatics, this review classifies applications and presents a summary of the latest results. Among them, we classify the applications of multilayer networks according to the object of study. Furthermore, because of the systemic nature of biology, we classify the subjects into several hierarchical categories, such as cells, tissues, organs, and groups, according to the hierarchical nature of biological composition. On the basis of the complexity of biological systems, we selected brain research for a detailed explanation. We describe the application of multilayer networks and chronological networks in brain research to demonstrate the primary ideas associated with the application of multilayer networks in biological studies. Finally, we mention a quality assessment method focusing on multilayer and single-layer networks as an evaluation method emphasizing network studies.