Amino acid network and its scoring application in protein-protein docking

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. (c) 2008 Elsevier B.V. All rights reserved.

由疏水残基和亲水残基组成的蛋白质 - 蛋白质复合物可分别被划分为疏水氨基酸网络结构和亲水氨基酸网络结构。在本文中，我们有兴趣分析这两种不同类型的网络，并发现这些网络具有小世界特性。由于复合物界面的特征互补性，蛋白质 - 蛋白质对接可被视为一种特殊的网络重连。正确对接的复合物构象的这些网络相较于不正确的网络，其度值有更大的增加，聚类系数有更大的衰减。因此，提出了两个基于网络参数的评分项，其中考虑了几何互补性、疏水 - 疏水以及极性 - 极性相互作用。与一个两项能量函数相比，一个包含这两个基于网络的评分项的简单评分函数HPNet在两个方面显示出优势，即不依赖于能量考量且具有更好的区分度。此外，将基于网络的评分项与一些其他能量项相结合，一个新的多项评分函数HPNet - combine也能够对RosettaDock的评分函数做出一些改进。（c）2008爱思唯尔有限公司。保留所有权利。