引入显式水分子对接提高蛋白质配体复合物结构的预测精度  

Docking with Explicit Water Improves Accuracy of the Prediction of Protein-Ligand Complexes

作　　者：徐维维[1] 吕强[1,2] 吴宏杰[1,2,3] 权丽君[1] 

机构地区：[1]苏州大学计算机科学与技术学院,江苏苏州215006 [2]江苏省计算机信息技术重点实验室,江苏苏州215006 [3]苏州科技学院电子与信息工程学院,江苏苏州215009

出　　处：《生物物理学报》2012年第12期983-997,934,共15页Acta Biophysica Sinica

基　　金：国家自然科学基金项目(60970055;61170125)

摘　　要：在蛋白质复合物界面一般都会存在着一定量的水分子,这些水分子通过空间占据和氢键方式影响蛋白质与配体的位置关系。应用现有的计算机方法研究蛋白质-配体对接时,一般不会显式地考虑水分子的作用。本文显式地将水分子引入蛋白质-配体对接过程,考虑水分子空间占据和氢键能量对复合物对接结构的影响,提出了一种包含水分子的蛋白质-配体对接算法。实验结果表明引入水分子使蛋白质-配体对接质量有明显提高。A certain amount of water molecules is often observed at the protein-ligand docking interface. These water molecules affect the docking mode through space occupation and forming hydrogen bonds. Current computational methods of predicting protein-ligand docking mode usually ignore the interaction between water molecules and complex. In this paper, the authors introduce an enhanced protein-ligand docking algorithm with explicit water-involved, which was taken into account two influences of water molecules including space occupation and hydrogen bonds. The results of experiments show that docking with explicit water-involved helps correct protein-ligand docking.

关 键 词：水分子 空间占据 氢键 蛋白质-配体对接 

分 类 号：Q61[生物学—生物物理学]