Del Carpio Carlos A, Qiang Pei, Ichiishi Eiichiro, Tsuboi Hideyuki, Koyama Michihisa, Hatakeyama Nozomu, Endou Akira, Takaba Hiromitsu, Kubo Momoji, Miyamoto Akira
Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-11-1302 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
Genome Inform. 2006;17(2):270-8.
A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the proposed algorithm. This is the first time this type of research has been reported. Application of the methodology to several protein complexes where remarkable backbone rearrangement is observed shows that the new algorithm is able to deal with the problem of change of backbone conformation at protein interaction. We have implemented the module within the system MIAX (Macromolecular interaction assessment computer system) and together with our already reported soft and flexible docking algorithms we have developed a powerful tool for protein function analysis as part of wide genome function evaluation.
引入了一种新算法来处理与其他蛋白质相互作用时蛋白质中环和结构域的分子内运动。该方法基于复杂能量景观采样和机器人运动规划。绘制蛋白质上的高灵活性区域是所提出算法的基础。这是首次报道此类研究。将该方法应用于几个观察到显著主链重排的蛋白质复合物，结果表明新算法能够处理蛋白质相互作用时主链构象变化的问题。我们已将该模块实现在系统MIAX（大分子相互作用评估计算机系统）中，并且与我们已经报道的软对接和灵活对接算法一起，我们开发了一个强大的蛋白质功能分析工具，作为广泛基因组功能评估的一部分。
