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

<div> <div>This dataset contains important data files for the MD simulation that are part of this publication.</div> <div>&nbsp;</div> <div>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.</div> <div>&nbsp;</div> <div>The directory "figure3" contains the raw data used to create Figure 3 in the manuscript.</div> <div>&nbsp;</div> <div>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.</div> <div>&nbsp;</div> <div>Subdirectory "b" contains a numpy array (.npy) with the data for the correlation heatmap in subfigure 3b.</div> <div>&nbsp;</div> <div>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:</div> <ul> <li>used: Already used sets of MD structures (frozenset)</li> <li>selection: Structure set selected in the last iteration (set)</li> <li>weights: weights of each structure in the selected structure set (numpy array)</li> <li>iteration: Counter of the last iteration (int)</li> </ul> <div>&nbsp;</div> <div>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.</div> </div> <p>&nbsp;</p>