Understanding the differences of Danusertib’s Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified Using Conventional and Enhanced Molecular Dynamics Simulations.
In this repository are available the initial structures of Aurora A and Aurora B in complex with Danusertib ligand in PDB format.
- The fingerprints must be previously calculated using the PL IFP Traj tool script.
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A routes.csv file should be prepared with the output paths of the processed trajectories as the example routes.csv.
Note: To obtain the paths, use the PL IFP Traj tool script. In the cell where the paths are read, the "trajectory" number and the path will be printed. Note that the order of the replicas to be used depends on the order in which the files are read in the analysis. Not always the "trajectory" 1 will correspond to the WT-MetaD replica1.
Save the information in the routes.csv file with the following structure:
trajectory,path
0,'/path_to_output/Traj4_0.3/rep01/ramd_trj_fixed.xtc'
1,'/path_to_output/Traj4_0.3/rep010/ramd_trj_fixed.xtc'
2,'/path_to_output/Traj4_0.3/rep011/ramd_trj_fixed.xtc'
3,'/path_to_output/Traj4_0.3/rep012/ramd_trj_fixed.xtc'
...
- The clusters will be obtained using the PL IFP Analysis tool, however, the PL IFP Analysis tool script should be modified, and a cell should be added at the end with the following code:
ifp_dataframe = df_ext[["time", "label", "Traj", "Repl"]]
ifp_dataframe.rename(columns={"time": "frame", "label": "cluster", "Traj": "traj", "Repl": "replica"}, inplace=True,)
ifp_dataframe.to_csv("IFP_data.csv")
These lines will write the IFP_data.csv file with the following information:
,frame,cluster,traj,replica
0,0,2,15,Traj4_0.3
1,3,2,15,Traj4_0.3
...
- Then the extract_frames.py script should be used to extract the structures in PDB files using MDAnalysis.
Use it as:
python extract_frames.py IPF_data.csv -r routes.csv -f 300
The input file is the IFP_data.csv. For the -r or --routes option, the routes.csv file should be provided, whereas the -f or --frames option correspond to the number of frames used for the fingerprints analysis.