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Amino acid network and its scoring application in protein–protein docking
- Source :
-
Biophysical Chemistry . May2008, Vol. 134 Issue 3, p111-118. 8p. - Publication Year :
- 2008
-
Abstract
- Abstract: Protein–protein complex, composed of hydrophobic and hydrophilic residues, can be divided into hydrophobic and hydrophilic amino acid network structures respectively. In this paper, we are interested in analyzing these two different types of networks and find that these networks are of small-world properties. Due to the characteristic complementarity of the complex interfaces, protein–protein docking can be viewed as a particular network rewiring. These networks of correct docked complex conformations have much more increase of the degree values and decay of the clustering coefficients than those of the incorrect ones. Therefore, two scoring terms based on the network parameters are proposed, in which the geometric complementarity, hydrophobic–hydrophobic and polar–polar interactions are taken into account. Compared with a two-term energy function, a simple scoring function HPNet which includes the two network-based scoring terms shows advantages in two aspects, not relying on energy considerations and better discrimination. Furthermore, combing the network-based scoring terms with some other energy terms, a new multi-term scoring function HPNet-combine can also make some improvements to the scoring function of RosettaDock. [Copyright &y& Elsevier]
- Subjects :
- *AMINO acids
*ORGANIC acids
*PROTEINS
*PEPTIDES
Subjects
Details
- Language :
- English
- ISSN :
- 03014622
- Volume :
- 134
- Issue :
- 3
- Database :
- Academic Search Index
- Journal :
- Biophysical Chemistry
- Publication Type :
- Academic Journal
- Accession number :
- 31561720
- Full Text :
- https://doi.org/10.1016/j.bpc.2007.12.005