Supplementary Information: Multimodal binding and inhibition of bacterial ribosomes by the 2 antimicrobial peptides Api137 and Api88

This dataset contains important data files for the MD simulation that are part of this publication. The "simulations" directory contains Gromacs parameter files (.mdp) and the run input files (.tpr) as well as the final coordinate files (.gro) of each individual production simulation. The directory "figure3" contains the raw data used to create Figure 3 in the manuscript. The subdirectory "a" contains the data for the PCA projection plot in subfigure 3a. It includes projections of the simulation ensembles of Api88 conformation I-III on to the two dominant conformational modes (.xvg) and the respective extreme conformations (.pdb). The projections of the three initial models and the optimized structure set are also included. Subdirectory "b" contains a numpy array (.npy) with the data for the correlation heatmap in subfigure 3b. Subdirectory "c" contains the results of several correlation-optimization searches. Each directory "N#_maps", where # is to be replaced by the number of structures in the set, contains the search results for N correlation-optimized structures in the Api88 trajectories in the form of a pickled python dictionary (state.pkl). The dictionary has the following keys: used: Already used sets of MD structures (frozenset) selection: Structure set selected in the last iteration (set) weights: weights of each structure in the selected structure set (numpy array) iteration: Counter of the last iteration (int) The directory "supplentary_figure_correlation_time" contains the data for a plot of the optimized correlation coefficient as a function of simulation time. The results of the optimization algorithms (as pickled python objects) are included in the subdirectories with the associated trajectory length as a name.本数据集包含本研究出版物配套的分子动力学（MD, Molecular Dynamics）模拟所需的重要数据文件。 `simulations` 目录包含各独立生产模拟的GROMACS参数文件（.mdp）、运行输入文件（.tpr）以及最终坐标文件（.gro）。 `figure3` 目录包含论文中图3绘制所用的原始数据。 子目录`a`包含子图3a的主成分分析（PCA, Principal Component Analysis）投影图所需数据，涵盖Api88构象I至III的模拟系综在两种主导构象模式上的投影数据（.xvg格式）、对应极端构象的结构文件（.pdb），同时包含三种初始模型与优化后结构集的投影数据。 子目录`b`包含子图3b相关性热图所需的数值Python（NumPy）数组文件（.npy）。 子目录`c`包含多次相关性优化搜索的结果。每个命名为`N#_maps`的子目录（其中`#`需替换为结构集中的结构数量），以Python序列化字典（state.pkl）的形式，存储Api88模拟轨迹中N个相关性优化结构的搜索结果。该字典包含以下键值： - `used`：已使用的MD结构集（不可变集合frozenset） - `selection`：最后一次迭代中选中的结构集（可变集合set） - `weights`：选中结构集中各结构的权重（NumPy数组） - `iteration`：最后一次迭代的计数器（整数int） `supplementary_figure_correlation_time` 目录包含优化后相关系数随模拟时间变化的绘图原始数据。优化算法的结果（以Python序列化对象形式存储）被存放于以对应轨迹长度命名的子目录中。