Evaluation on performance of MM/PBS A in nucleic acid-protein systems

• 作者: Yuan-Qiang Chen Yan-Jing Sheng Hong-Ming Ding Yu-Qiang Ma
• 来源期刊: 中国物理B（英文版）
• 年，卷（期）: 2022,（4）
• 所属期刊栏目: INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY
• 页码范围: 826-831
• 页数: 6页
• 语种: 英文
• DOI: 10.1088/1674-1056/ac3a5c

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/PBS A 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/PBS A.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBS A)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.