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Int. J. Mol. Sci. 2011, 12(12), 8773-8786; doi:10.3390/ijms12128773
Article

Scoring Function Based on Weighted Residue Network

1,†,*  and 2,†
Received: 27 September 2011; in revised form: 4 November 2011 / Accepted: 28 November 2011 / Published: 2 December 2011
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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 neighbors’ degree. Based on this weighted network model and these two parameters, a new docking scoring function is proposed in this paper. The scoring and ranking for 42 systems’ bound and unbounded docking results are performed with this new scoring function. Comparing the results obtained from this new scoring function with that from the pair potentials scoring function, we found that this new scoring function has a similar performance to the pair potentials on some items, and this new scoring function can get a better success rate. The calculation of this new scoring function is easy, and the result of its scoring and ranking is acceptable. This work can help us better understand the mechanisms of protein-protein interactions and recognition.
Keywords: residue network; weighted parameter; protein-protein docking; scoring function residue network; weighted parameter; protein-protein docking; scoring function
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Jiao, X.; Chang, S. Scoring Function Based on Weighted Residue Network. Int. J. Mol. Sci. 2011, 12, 8773-8786.

AMA Style

Jiao X, Chang S. Scoring Function Based on Weighted Residue Network. International Journal of Molecular Sciences. 2011; 12(12):8773-8786.

Chicago/Turabian Style

Jiao, Xiong; Chang, Shan. 2011. "Scoring Function Based on Weighted Residue Network." Int. J. Mol. Sci. 12, no. 12: 8773-8786.



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