摘要
The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.
作者
陈远强
盛艳静
丁泓铭
马余强
Yuan-Qiang Chen;Yan-Jing Sheng;Hong-Ming Ding;Yu-Qiang Ma(Center for Soft Condensed Matter Physics and Interdisciplinary Research,School of Physical Science and Technology,Soochow University,Suzhou 215006,China;National Laboratory of Solid State Microstructures and Department of Physics,Collaborative Innovation Center of Advanced Microstructures,Nanjing University,Nanjing 210093,China)
基金
Project supported by the National Natural Science Foundation of China(Grant Nos.11874045 and 11774147)。