Elucidation of protein-ligand interactions by multiple trajectory analysis methods

Nian Wu*, Ruotian Zhang, Xingang Peng, Lincan Fang, Kai Chen, Joakim S. Jestilä

*Tämän työn vastaava kirjoittaja

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

14 Lataukset (Pure)

Abstrakti

The identification of interaction between protein and ligand including binding positions and strength plays a critical role in drug discovery. Molecular docking and molecular dynamics (MD) techniques have been widely applied to predict binding positions and binding affinity. However, there are few works that describe the systematic exploration of the MD trajectory evolution in this context, potentially leaving out important information. To address the problem, we build a framework, Moira (molecular dynamics trajectory analysis), which enables automating the whole process ranging from docking, MD simulations and various analyses as well as visualizations. We utilized Moira to analyze 400 MD simulations in terms of their geometric features (root mean square deviation and protein-ligand interaction profiler) and energetics (molecular mechanics Poisson-Boltzmann surface area) for these trajectories. Finally, we demonstrate the performance of different analysis techniques in distinguishing native poses among four poses.

AlkuperäiskieliEnglanti
Sivut6903-6915
Sivumäärä13
JulkaisuPhysical Chemistry Chemical Physics
Vuosikerta26
Numero8
Varhainen verkossa julkaisun päivämäärä5 helmik. 2024
DOI - pysyväislinkit
TilaJulkaistu - 5 helmik. 2024
OKM-julkaisutyyppiA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä

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