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Chin. Phys. B, 2022, Vol. 31(4): 048701    DOI: 10.1088/1674-1056/ac3a5c

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

Yuan-Qiang Chen(陈远强)1, Yan-Jing Sheng(盛艳静)1, Hong-Ming Ding(丁泓铭)1,†, and Yu-Qiang Ma(马余强)2,‡
1 Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China;
2 National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
Abstract  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.
Keywords:  molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA)      screening electrostatic interaction      protein      nucleic acid      molecular dynamics simulation  
Received:  11 October 2021      Revised:  11 November 2021      Accepted manuscript online:  17 November 2021
PACS:  87.14.E- (Proteins)  
  87.14.G- (Nucleic acids)  
  87.15.A- (Theory, modeling, and computer simulation)  
  87.15.kj (Protein-polynucleotide interactions)  
Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11874045 and 11774147).
Corresponding Authors:  Hong-Ming Ding, Yu-Qiang Ma     E-mail:;

Cite this article: 

Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强) Evaluation on performance of MM/PBSA in nucleic acid-protein systems 2022 Chin. Phys. B 31 048701

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