Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes

Molecules

Feng Qiu¹  Ya Gao²  Tong Zhu³  Na Li³ 

[1] Institute of Artificial Intelligence on Education, Shanghai Normal University, Shanghai 200234, China;School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China;Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China;

关键词: G-Quadruplex;    molecular dynamics simulation;    force field;    polarization effect;   

DOI  :  10.3390/molecules26175379

来源: DOAJ

【 摘 要 】

G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer target and their application in material science. Molecular dynamics (MD) simulation is the key theoretical tool in the study of GQ’s structure-function relationship. In this article, we systematically benchmarked the five force fields of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 on the MD simulation of G-quadruplex from four aspects: structural stability, central ion channel stability, description of Hoogsteen hydrogen bond network, and description of the main chain dihedral angle. The results show that the overall performance of the Drude force field is the best. Although there may be a certain over-polarization effect, it is still the best choice for the MD simulation of G-quadruplexes.

【 授权许可】

Unknown