期刊
CHINESE PHYSICS B
卷 31, 期 4, 页码 -出版社
IOP Publishing Ltd
DOI: 10.1088/1674-1056/ac3a5c
关键词
molecular mechanics; Poisson-Boltzmann surface area (MM; PBSA); screening electrostatic interaction; protein; nucleic acid; molecular dynamics simulation
资金
- National Natural Science Foundation of China [11874045, 11774147]
The study demonstrated that using screening electrostatic energy in molecular mechanics can greatly improve the performance of MM/PBSA in predicting binding energy, especially in highly charged biological systems. This highlights the potential power of the screening MM/PBSA method for accurately predicting binding affinity.
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.
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