物理化学学报 >> 2002, Vol. 18 >> Issue (11): 1052-1056.doi: 10.3866/PKU.WHXB20021119

研究简报 上一篇    

基于分子表面的水化自由能预测方法

侯廷军;徐筱杰   

  1. 北京大学化学与分子工程学院,北京 100871
  • 收稿日期:2002-02-01 修回日期:2002-06-28 发布日期:2002-11-15
  • 通讯作者: 徐筱杰 E-mail:xiaojxu@chem.pku.edu.cn

Aqueous Solvation Models Based on Accessible Surface Area Calculations

Hou Ting-Jun;Xu Xiao-Jie   

  1. College of Chemistry and Molecular Engineering, Peking University, Beijing 100871
  • Received:2002-02-01 Revised:2002-06-28 Published:2002-11-15
  • Contact: Xu Xiao-Jie E-mail:xiaojxu@chem.pku.edu.cn

摘要: 报导了一种基于加权原子表面的水合自由能预测(SAWSA).对于不同原子类型的溶剂化参数,其参数化分为三个步骤:首先用SMARTS 语言确定不同的原子类型;然后计算每个原子的溶剂可及化表面;最后用遗传算法来优化不同原子类型的溶剂化参数.采用该模型,计算了18个蛋白质分子的水合自由能,预测结果和PB/SA的计算结果呈现了很好的线性关系(r=0.99).计算表明,SAWSA模型对有机小分子和生物大分子都具有很好的预测能力.

关键词: 水化自由能, 溶剂效应, 分子表面, 遗传算法, 原子类型定义

Abstract: An empirical solvation model based on atom-weighted accessible surface areas was reported. This solvation model is based on atom-weighted solvent accessible surface area (SAWSA). The parameterization procedure for different kind of atoms was performed as follows: firstly, the atoms in a molecule were defined to different atom types based on SMARTS language; then, solvent accessible surface area for each atom was calculated; finally, a genetic algorithm (GA) was applied to optimize the solvation parameters for different atom types. The SAWSA model was applied to predict the aqueous salvation free energies for 18 proteins. The solvation free energies predicted by the SAWSA model show high linear correlation (r=0.99) with those predicted by PB/SA. The calculated results indicate that the SAWSA model bears significant predicted ability to small organic molecules and proteins.

Key words: Aqueous solvation free energy, Solvation effect, Molecular surface