This package contains the analysis script and the raw data to reproduce the results from the first demo of Nostrum's web app. It consists on using the latest version of Nostrum web app to reproduce some of the computational results published in this Nature Catalysis article. Our goal is to predict the relative activity of different compounds with our computational methods and find certain correlations with experimental data reported in this study.
To analyze the simulations a Python script is available in this repository. Find below the instructions to run it.
The analysis script requires the following:
- Python 2.7 or higher or Python 3.1 or higher must be installed.
- The Pandas and NumPy libraries are required.
The script calculates the number and frequency of accepted and total catalytic poses (with the -A CATE option) along the PELE simulation. To use it, you have to pass the path of the report files in the input ( -i PATH ) flag, specify the distance thresholds for the key substrate-enzyme distance ( -TE FLOAT ) and the critical distances between catalytic residues ( -CD FLOAT ), and pick the column numbers of the serine-substrate, serine-histidine, and histidine-acid distances ( -CE I1 I2 I3 , the indexing is 1-based). The output name can be specified with the -o STRING flag, and the process can be run in parallel ( -NP NUM_OF_THREADS ). An example would be like this:
python PELEAnalyzer.py -i PATH_TO_THE_REPORT_FILES -TE 4.5 -CD 4.5 -CE 8 9 10 -NP 16 -A CATE -o OUTPUT
For more information on how to use the script or other options, use the -h flag to get the help message.
## Examples
python PELEAnalyzer.py -i output/FraCm2_MHET/induced_fit_refinement/6_adaptive_pele_simulation/complex_2/output/*/report* -TE 4.5 -CD 4.5 -CE 8 9 10 -V -NP 1 -A NRA -o MHET_FraCm2
python PELEAnalyzer.py -i output/FraCm2_PAE/induced_fit_refinement/6_adaptive_pele_simulation/complex_2/output/*/report* -TE 4.5 -CD 4.5 -CE 8 9 10 -V -NP 1 -A NRA -o PAE_FraCm2
python PELEAnalyzer.py -i output/FraCm2_GRP/induced_fit_refinement/6_adaptive_pele_simulation/complex_2/output/*/report* -TE 4.5 -CD 4.5 -CE 8 11 12 -V -NP 1 -A NRA -o GRP_FraCm2 -NE 3
python PELEAnalyzer.py -i output/FraCm2_VIN/induced_fit_refinement/6_adaptive_pele_simulation/complex_2/output/*/report* -TE 4.5 -CD 4.5 -CE 8 9 10 -V -NP 1 -A NRA -o GRP_FraCm2