Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
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DOI：
10.1002/prot.20572
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发表时间：
2005-08-01
影响因子：
2.9
通讯作者：
Umeyama, H
中科院分区：
文献类型：
--
作者：
Terashi, G;Takeda-Shitaka, M;Umeyama, H
在 CAPRI 第 1 轮和第 2 轮中，我们假设由于存在许多离子电荷会削弱活细胞中的静电相互作用力，因此疏水相互作用力可能在熵方面很重要。第 1 轮和第 2 轮的结果是，对结合位点和几何中心的预测是可以接受的，但对结合轴的预测很差，因为仅使用最大的苯簇来生成初始对接结构。这些是通过受体和配体表面上形成的苯簇的拟合而产生的。在CAPRI第3-5轮中，采用蛋白质-蛋白质相互作用表面上的网格评分和以及容易进入蛋白质-蛋白质相互作用区域的氨基酸残基的成对势作为计算方法，以及参与苯簇拟合的较小苯簇。靶点11和12得到了良好的预测模型。当建模的受体蛋白叠加在实验结构上时，模型和实验结构之间的RMSD对应的最小配体均方根偏差（RMSD）值分别为6.2 A和7.3 A。 (c) 2005 年 Wiley-Liss, Inc.
In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3-5, the grid-scoring sum on the protein-protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein-protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 A and 7.3 A, respectively. (c) 2005 Wiley-Liss, Inc.