R programming language environment version 3

We utilized UCSF Chimera 1.15 [39 (link)] to visualize the whole picture of LNP, whereas Discovery Studio Visualizer v21.10.020298 (Dassault Systèmes, San Diego, CA, USA) was used to visualize the detailed molecular interactions. Graphs were generated using tidyr [40 ], ggplot2 [41 ], ggforce [41 ], gridExtra [42 ], ggpubr [43 ], and patchwork [44 ] packages on Jupyter Notebook 6.4.7 [45 (link)] (Project Jupyter, Berkeley, CA, USA) under an R programming language environment version 3.6.1 (R Foundation for Statistical Computing, Vienna, Austria) [46 ]. Artworks were created using Inkscape 1.1.1 [47 ] (The Inkscape Project, Boston, MA, USA).

The ccptraj program in AmberTools21 was employed for MD trajectory analyses. The analyses include root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and conventional H-bond conservation. Molecular dynamics simulation trajectories were assessed using VMD. The ante-MMPBSA.py in AmberTools21 was used to calculate MMGBSA binding energy and decomposition analysis. To compute contact surface analysis (CSA), we used the dr_sasa program [53 (link)]. Jupyter Notebook 6.4.7 (Project Jupyter, Berkeley, CA, USA) [63 (link)] was used to conduct analyses under an R programming language environment version 3.6.1 (R Foundation for Statistical Computing, Vienna, Austria) [64 ]. Statistical analyses were performed using an R package, rstatix [65 ]. Hierarchical clustering on principal analysis (HCPC) for RMSD was carried out using an R package, bio3d [66 (link)], while for RMSF, FactoMineR [67 (link)] and factoExtra [68 ] were used. Graphs were generated using R packages tidyr [69 ], ggplot2 [70 ], and ggpubr [71 ]. Inkscape 1.3 (The Inkscape Project, Boston, MA, USA) [72 ] was used to create the visual illustrations.