Acta Phys. -Chim. Sin. ›› 2002, Vol. 18 ›› Issue (11): 1052-1056.doi: 10.3866/PKU.WHXB20021119

• Note • Previous Articles    

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

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