BADock

Prediction of protein interactions binding affinity from unbound tertiary structures

Getting Started

BADock/db: Contains the two datasets used in the analysis, Affinity Benchmark 2 and Docking Benchmark 5
BADock/src: Contains the source code
BADock/workspace: Contains the results of the analysis
BADock/revision: Contains the analysis of the revision

Prediction of binding affinities using all the docking poses from the unbound protein structures.

setup_submitter.py: Script that permits to perform the docking of the structures and scoring of the obtained poses in the whole dataset.
- Using the option 'docking', it executes setup_docking.py, which runs Patchdock to obtain the docking poses (decoys), and runs Fiberdock to refine and rescore the decoys. Example:
```
python /path/to/BADock/src/Binding_Affinity_Docking/setup_submitter.py -s docking
```
- Using the option 'scoring', it executes setup_score.py, which scores the decoys using the statistical potentials EPAIR, ES3DC and E3D. Example:
```
python /path/to/BADock/src/Binding_Affinity_Docking/setup_submitter.py -s docking
```
setup_docking.py: Runs Patchdock to obtain the docking poses and Fiberdock to refine and rescore them.
setup_score.py: Scores the decoys using statistical potentials.

Until here, it is not necessary to run the scripts because the results are already in BADock/workspace)
score_nativecomplex.py: Scores the native complexes of the dataset.
affinity_analysis.py: Performs the prediction of binding affinities using the statistical potentials.
CCharPPI_affinityparse.py: Performs the prediction of binding affinities using the CCharPPI server results.

Analysis of the conformational space of the encounter complexes in four classes (Near-Native, Face-Face, Face-Back and Back-Back).

setup_submitter.py: Script that permits to submit the different parts of the Binding Mechanism Docking analysis in a computer cluster.
setup_decoys.py: Runs Patchdock to obtain the docking poses of the Docking Benchmark 5 and Fiberdock to refine and rescore them.
setup_decoys.py: Runs Patchdock to obtain the docking poses of the Docking Benchmark 5 and Fiberdock to refine and rescore them.
setup_location.py: Calculates the location (Near-Native, Face-Face, Face-Back and Back-Back) for each decoy of each protein in the Docking Benchmark 5.
setup_score.py: Scores the decoys using statistical potentials.

Until here, it is not necessary to run the scripts because the results are already in BADock/workspace)
analyze_scores.py: Get the scores of each decoy for each protein-protein interaction and analyze the different locations (Near-Native, Face-Face, Face-Back and Back-Back) .
print_score_results.py: Plot the boxplots of scores depending on the location (Near-Native, Face-Face, Face-Back and Back-Back) (Figure 1, Supplementary Figures S2, S3, S4).
plot_method_example.py: Plot the figures of the examples of decoy classification by location (Supplementary Figure S1).
show_byprotein.py: Print the score distributions of each location for each PPI.

Python library used for the analyses of BADock.

ba_jobs: Folder containing the Affinity results of all the protein-protein interactions in Affinity Benchmark 2.
img: Folder containing the resulting images.
CCharPPI_AffinityBenchmark.csv: File containing the scores from the CCharPPI server
scores_native.txt: File containing the scores of the native decoys

benchmark5_jobs: Folder containing the Mechanisms results of all the protein-protein interactions in Docking Benchmark 5.
figures: Folder containing the resulting images.
figure_method.csv: File containing the images of the examples of location (from plot_method_example.py).
scores_locations_E+OX.txt: File containing the scores of the protein-protein interactions

This folder contains all the results asked in the revision and includes a report of these changes explaining them and how to obtain them.

revision_questions_report.pdf: Report explaining the major changes in the review
Figures: Folder containing the figures included in the review
Tables: Folder containing the tables included in the review

This folder contains all the source code to obtain the changes of the review and includes a README explaining how to execute the scripts.

README: Report explaining how to execute the scripts of the changes in the revision