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

ABSTRACT: 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.

SUBMITTER: Li N

PROVIDER: S-EPMC8434458 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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

Li Na N Gao Ya Y Qiu Feng F Zhu Tong T

Molecules (Basel, Switzerland) 20210904 17

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 Hoo ...[more]

PMID: 34500812

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