Kanamori Eiji, Murakami Yoichi, Tsuchiya Yuko, Standley Daron M, Nakamura Haruki, Kinoshita Kengo
Japan Biological Information Research Center, Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Proteins. 2007 Dec 1;69(4):832-8. doi: 10.1002/prot.21737.
We have developed a new method to predict protein- protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the interacting residues. The optimization is carried out using a genetic algorithm in combination with Monte Carlo sampling. We applied this method to CAPRI targets and evaluated the performance systematically. Consequently, our method could achieve native-like predictions in several cases. In addition, we have analyzed the feasibility of the ET method for docking simulations, and found that the conservation information was useful only in a limited category of proteins (signal related proteins and enzymes).
我们开发了一种基于分子表面形状互补性以及通过进化追踪（ET）分析获得的序列保守性来预测蛋白质-蛋白质复合物的新方法。对接是通过优化一个目标函数来实现的，该目标函数评估由相互作用残基的保守性加权的形状互补程度。使用遗传算法结合蒙特卡罗采样进行优化。我们将此方法应用于CAPRI靶标并系统地评估了其性能。结果，我们的方法在几种情况下能够实现类似天然结构的预测。此外，我们分析了ET方法用于对接模拟的可行性，发现保守性信息仅在有限类别的蛋白质（信号相关蛋白和酶）中有用。
