Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophob...Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophobic and the hydrophilic residue networks. By analyzing the network parameters, it is found that the correct binding complex conformations are of both higher sum of the interface degree values and lower characteristic path length than those incorrect ones. These features reflect that the correct bind-ing complex conformations have better geometric and/or residue type complementarity, and the correct binding modes are very important for preserving the characteristic path lengths of native protein complexes. In addition, two scoring terms are proposed based on the network parameters, in which the characteristics of the entire complex shape and residue type complementarity are taken into account. These network-based scoring terms have also been used in conjunction with other scoring terms, and the new multi-term scoring HPNCscore is devised in this work. It can improve the discrimination of the combined scoring function of RosettaDock more than 12%. This work might enhance our knowledge of the mechanisms of protein-protein interactions and recognition.展开更多
We investigate the dynamical behavior of aftershocks in earthquake networks, and the earthquake network calculated from a time series is constructed by contemplating cell resolution and temporal causality. We attempt ...We investigate the dynamical behavior of aftershocks in earthquake networks, and the earthquake network calculated from a time series is constructed by contemplating cell resolution and temporal causality. We attempt to connect an earthquake network using relationship between one main earthquake and its aftershocks from seismic data of California. We mainly examine some topological properties of the earthquake such as the degree distribution, the characteristic path length, the clustering coefficient, and the global efficiency. Our result cannot presently determine the universal scaling exponents in statistical quantities, but the topological properties may be inferred to advance and improve by implementing the method and its technique of networks. Particularly, it may be dealt with a network issue of convenience and of importance in the case how large networks construct in time to proceed on earthquake systems.展开更多
基金supported by the National Natural Science Foundation of China (Grant Nos. 20773006, 30670497, 10974008)Beijing Natural Science Foundation (Grant No. 4102006) Specialized Research Fund for the Doctoral Program of Higher Education (Grant No. 200800050003)
文摘Residue networks are constructed by defining the residues as the vertices and atom contacts between them as the edges. The residue network of a protein complex is divided into two types of networks, i.e. the hydrophobic and the hydrophilic residue networks. By analyzing the network parameters, it is found that the correct binding complex conformations are of both higher sum of the interface degree values and lower characteristic path length than those incorrect ones. These features reflect that the correct bind-ing complex conformations have better geometric and/or residue type complementarity, and the correct binding modes are very important for preserving the characteristic path lengths of native protein complexes. In addition, two scoring terms are proposed based on the network parameters, in which the characteristics of the entire complex shape and residue type complementarity are taken into account. These network-based scoring terms have also been used in conjunction with other scoring terms, and the new multi-term scoring HPNCscore is devised in this work. It can improve the discrimination of the combined scoring function of RosettaDock more than 12%. This work might enhance our knowledge of the mechanisms of protein-protein interactions and recognition.
文摘We investigate the dynamical behavior of aftershocks in earthquake networks, and the earthquake network calculated from a time series is constructed by contemplating cell resolution and temporal causality. We attempt to connect an earthquake network using relationship between one main earthquake and its aftershocks from seismic data of California. We mainly examine some topological properties of the earthquake such as the degree distribution, the characteristic path length, the clustering coefficient, and the global efficiency. Our result cannot presently determine the universal scaling exponents in statistical quantities, but the topological properties may be inferred to advance and improve by implementing the method and its technique of networks. Particularly, it may be dealt with a network issue of convenience and of importance in the case how large networks construct in time to proceed on earthquake systems.
