scoring function based on weighted residue network得分函数基于加权残数网络.pdfVIP

Int. J. Mol. Sci. 2011, 12, 8773-8786; doi:10.3390/ijm OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 /journal/ijms Article Scoring Function Based on Weighted Residue Network Xiong Jiao 1,†,* and Shan Chang 2,† 1 Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan 030024, China 2 College of Informatics, South China Agricultural University, Guangzhou 510642, China; E-Mail: schang@ † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: jiaoxiong@; Tel.: +86-351-6010818. Received: 27 September 2011; in revised form: 4 November 2011 / Accepted: 28 November 2011 / Published: 2 December 2011 Abstract: Molecular docking is an important method for the research of protein-protein interaction and recognition. A protein can be considered as a network when the residues are treated as its nodes. With the contact energy between residues as link weight, a weighted residue network is constructed in this paper. Two weighted parameters (strength and weighted average nearest neighbors’ degree) are introduced into this model at the same time. The stability of a protein is characterized by its strength. The global topological properties of the protein-protein complex are reflected by the weighted average nearest ne