Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB

Data and plotting script for the research article "Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB". All data are analyzed by cpptraj (water accessibility), mdpocket (pocket size detection), and pytraj. Pocket size can be calculated using pocket_multi_holo/nsub.sh.  The main analysis is performed by a python class SpsB_simulation_analysis() in ./analyze_interaction.py with multi.sh. This script generates a pickle file for each simulated system (1us * 5 replcates) which can be read by the main plotting ipynb file SpsB_analysis_clean.ipynb. 

Due to the large filesize, the not all trajectories are not uploaded here ( > 100GB in total). Instead, only the water-stripped trajectories of the first (out of five) simulations are uploaded. The rest of the simulations can be inquired upon reasonable request.

PDB files to generate Figure 1f are deposited as figure1f_lowerleft/lowerright/upperright.pdb. 

The sampling densities of the PK150 ligands are stored in the .dx format. To reproduce the Figure 3d and Figure 3e in the manuscript. Download all .dx files, .vmd files, RSL_wt.pdb and RL.pdb. Running vmd with "vmd -e RL_PK150_volume.vmd" reproduces Figure 3d and "vmd -e RSL_PK150_volume.vmd" reproduces Figure 3d and