物理化学学报 >> 2006, Vol. 22 >> Issue (05): 622-626.doi: 10.1016/S1872-1508(06)60023-5

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针对蛋白质复合物Other类型的打分函数

沈龙珠;李春华;马晓慧;常珊;陈慰祖;王存新   

  1. 北京工业大学生命科学与生物工程学院,北京100022
  • 收稿日期:2005-11-17 修回日期:2006-02-16 发布日期:2006-04-28
  • 通讯作者:

Scoring Function for the Other-type Protein Complexes

SHEN Long-Zhu;LI Chun-Hua MA Xiao-Hui;CHANG Shan;CHEN Wei-Zu;WANG Cun-Xin;   

  1. College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, P. R. China
  • Received:2005-11-17 Revised:2006-02-16 Published:2006-04-28
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摘要： 在不同类型复合物结合界面的物理化学特征不同的基础上, 针对较难预测的Other 类型复合物设计出特异性打分函数, 用于在对接过程中挑选出有效结构. 该函数由原子接触能(EACE)、范德华和静电相互作用能组成,通过多元线性回归方法获得各项的权重系数. 对来自CAPRI benchmark1 中17 个Other 类复合物例子进行打分测试. 结果表明,组合打分能够刻画出Other 类型复合物单体间相互作用的特征, 反映出复合物形成前后的能量变化, 具备一定的从众多样本中筛选出有效结构的能力. 相对于残基成对势(RP), 该组合打分获得了更高的打分成功率. 对CAPRI 第八轮竞赛中两个结构预测模型进行打分排序, 该组合打分也体现出强于RP 的鉴别有效结合模式潜力.

关键词: 打分函数, 原子接触能, 残基成对势, Other 类复合物, CAPRI

Abstract: Based on the conclusion that different complexes have distinctive chemo-physical characters at interfaces,a specific scoring function was designed to select the effective structures in protein-protein docking procedure for the Other-type protein complexes, which are hard to predict. This scoring function was composed of the atomic contact energy (EACE), van der Waals, and electrostatic interaction energies. The weight of each term was obtained by the multiple linear regression approach. The test result on 17 Other-type complexes from CAPRI benchmark1 demonstrated that the combinatorial scoring function could delineate the interaction feature of the Other-type complexes and reflect the energy change during the complex formation, and it has certain capacity of discriminating effective structures fromnumbers of the docked modes. Compared to the residue pair potential (RP), the combinatorial score could gain a higher success rate. Ranking the predicted models of two targets in CARPI round 8, the combinatorial score also exhibits greater potential to distinguish the effective association modes.

Key words: Scoring function, Atomic contact energy, Residue pair potential, Other-type complexes, CAPRI