Predicting Binding Free Energy for Protein Complexes.
A novel empirical free energy function and a computationally more effect algorithm are applied to 21 protein complexes to predict the free energies of binding. Compared with the other works what have done in literature, better agreement between the predicted and measured binding free energies is obtained. The predicted values, are typically within 1.0 kcal/mol of the measured, while keeping a high correlation coefficient of 96 %. Predicting the binding free energy of a typical protease-inhibitor complex takes about 2 min on SGI-IMPACT R10000 Workstation. What is more, the results reconfirm that the interactions between the hydrophilic atoms may play a more favorable role in binding than in folding.
Tang
Hai-Xu
HX
Shanghai Institute of Biochemistry, the Chinese Academy of Sciences, Shanghai 200031, China. dingdafu@server.shcnc.ac.cn
Chen
Jie
J
Ding
Da-Fu
DF