Protein-protein interactions and recognition play a pivotal role in molecular biology. Molecular docking technology is an approach on protein-protein interaction and recognition. In the mechanism study and docking prediction of protein-protein interactions, the protein topology is often found important. Since the network tools can be used to take account of the global topological characteristics of the protein-protein complex, this method makes it easy to explain the structure mechanisms of protein-protein interactions. The three-dimensional structure of a protein can be treated as a complex network composed of residues. The front cover shows the three-dimensional structures of protein complex and the corresponding residue network representations. In the docking process, many complex structures will be produced, and the few correct docked complex conformations have different structures from those incorrect ones. Due to the characteristic complementarity of the complex interfaces, protein-protein docking can be viewed as a particular network rewiring. It is found that these networks of correct docked complex conformations have much more increase sum of the interface degree values and decay of characteristic path length than those of the incorrect ones. These network properties may help us to discriminate near-native structure from the incorrect ones and provide some insight into the future development of the scoring functions on protein-protein complex (see the article by CHANG Shan et al. on page 814).
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