节点文献
11种结合自由能评价函数对中草药中法尼酯受体的配体预测比较
Comparative studies of prediction of herb-based FXR ligands by 11 binding free energies scoring fuctions
【摘要】 以蛋白质晶体结构数据库PDB中FX-fexaramine复合物(PDB代码:1OSH)三维结构为研究对象,采用Ligandfit作为采样工具,筛选到中草药中12个可能与FXR相互作用强的的配体。并比较了11种结合自由能评价函数(Ligscorel、Lig- score2、D-Score、-PLP1、-PLP2、Jain、-PMF、Ludil、Ludi2、Ludi3,以及共同评价函数)在该研究体系中的预测能力。结果表明将评价函数中的-PLP1和-PLP1这2种评价函数的预测能力最好。
【Abstract】 Based on the optimized complex structure of FXR bound with specific ligand-fexaramine (PDB code 1OSH) , computer-aided structure-based virtual screening against Peking University Drug Design System (PKUDDS) was conducted to determine the occurrence of herb-based FXR ligands. 11 scoring functions (igscorel, Ligscore2, D-Score, -PLP1, -PLP2, Jain,-PMF, Ludil, Ludi2, Lu-di3 and consensus) have been compared to evaluate their prediction ability after conformational sampling by program Ligandfit. The results suggest that -PLP1 and -PLP2 have better prediction ability than others.
【Key words】 binding free energy； molecular docking； scoring function； Farnesoid X receptor； traditional Chinese medicine；
- 【文献出处】 计算机与应用化学 ,Computers and Applied Chemistry , 编辑部邮箱 ,2007年01期
- 【分类号】R284
- 【被引频次】10
- 【下载频次】313