基于原子表面的蛋白质水合自由能预测模型

提出了一种计算蛋白质水合自由能的简化模型（SAWSA 2）.模型把蛋白质分子中的原子分为20种不同的原子类型,通过每类原子的溶剂可及化表面以及相应的溶剂化参数,就可以得到分子的水合自由能.不同原子类型的溶剂化参数通过110个蛋白质分子水合自由能拟合得到,水合自由能的标准值采用了基于求解Possion-Boltzmann方程（PB）以及分子表面计算（SA） 相结合的方法.采用得到的模型,预测了20个蛋白质分子的水合自由能,预测值的相对值和绝对值都能和PB/SA的计算值很好地吻合,大大优于两种已报导的水合自由能模型.

Empirical Aqueous Solvation Model for Protein Based on Accessible Surface Areas

A simplified aqueous solvation model (SAWSA 2) for protein was develo ped.The model classified the atoms in protein into 20 basic types;and the aqueou s free energies of solvation was calculated by solvent-accessible surface areas of each atom type and corresponding solvation parameters.The solvation paramete r for each atom type was obtained by fitted the calculated aqueous free energies of solvation from PB/SA of 110 proteins.The solvation model developed in this w ork was applied to predict the solvation free energies of 20 proteins.The predic ted values from SAWSA 2 model were in good agreement with those from PB/SA model ,and were much better than those given by the two models previously reported.