├── LICENSE ├── PDBminer ├── PDBminer.py ├── PDBminer2coverage.py ├── PDBminer2network.py └── __init__.py ├── PDBminer_complex_filter ├── README.md ├── examples │ ├── P04637 │ │ ├── P04637_all.csv │ │ ├── P04637_filtered.csv │ │ ├── P04637_filtered_DBD.csv │ │ ├── P04637_filtered_DBD_interface.csv │ │ ├── P04637_filtered_interface.csv │ │ └── readme_P04637.txt │ ├── P78352 │ │ ├── P78352_all.csv │ │ ├── P78352_filtered.csv │ │ ├── P78352_filtered_interface.csv │ │ └── readme_P78352.txt │ └── find_PDBminer_complexes.py └── find_PDBminer_complexes.py ├── README.md ├── REPRODUCE_PAPER ├── TIMING │ ├── 1core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 2core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 3core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 4core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 5core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── 6core │ │ ├── input_file.csv │ │ ├── log.txt │ │ └── results │ │ │ ├── O75385 │ │ │ └── O75385_all.json │ │ │ ├── P10415 │ │ │ └── P10415_all.json │ │ │ ├── P28698 │ │ │ └── P28698_all.json │ │ │ ├── P40692 │ │ │ └── P40692_all.json │ │ │ ├── P48052 │ │ │ └── P48052_all.json │ │ │ ├── P62937 │ │ │ └── P62937_all.json │ │ │ ├── P62942 │ │ │ └── P62942_all.json │ │ │ ├── Q05397 │ │ │ └── Q05397_all.json │ │ │ ├── Q07817 │ │ │ └── Q07817_all.json │ │ │ ├── Q12931 │ │ │ └── Q12931_all.json │ │ │ ├── Q99856 │ │ │ └── Q99856_all.json │ │ │ └── Q9GZQ8 │ │ │ └── Q9GZQ8_all.json │ ├── time.csv │ └── time.py ├── TP53_CASESTUDY │ ├── input_file.csv │ ├── log.txt │ ├── readme.txt │ └── results │ │ └── P04637 │ │ ├── P04637_all.json │ │ ├── all_coverage_plot.pdf │ │ └── all_network.pdf └── readme.txt ├── examples ├── command_line │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ │ └── P22307 │ │ ├── P22307_all.json │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ └── all_network.pdf ├── csv_output │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ │ ├── O15520 │ │ ├── O15520_all.csv │ │ ├── all_coverage_plot.pdf │ │ └── all_network.pdf │ │ └── O75385 │ │ ├── O75385_all.csv │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ ├── all_coverage_plot_chunk_2.pdf │ │ └── all_network.pdf ├── different_clusters │ ├── do.sh │ ├── input_file_clusters.csv │ ├── log.txt │ └── results │ │ └── P22307 │ │ ├── P22307_all.json │ │ ├── P22307_cluster_1.json │ │ ├── P22307_cluster_2.json │ │ ├── P22307_filtered.json │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ ├── all_network.pdf │ │ ├── filtered_coverage_plot_cluster_1_chunk_0.pdf │ │ ├── filtered_coverage_plot_cluster_1_chunk_1.pdf │ │ ├── filtered_coverage_plot_cluster_2_chunk_0.pdf │ │ └── filtered_coverage_plot_cluster_2_chunk_1.pdf ├── input_file │ ├── do.sh │ ├── input_file.csv │ ├── log.txt │ └── results │ │ ├── P0A7Y7 │ │ ├── P0A7Y7_all.json │ │ ├── P0A7Y7_cluster_1.json │ │ ├── P0A7Y7_filtered.json │ │ ├── all_coverage_plot.pdf │ │ └── filtered_coverage_plot_cluster_1.pdf │ │ └── P11532 │ │ ├── P11532_all.json │ │ ├── all_coverage_plot_chunk_0.pdf │ │ ├── all_coverage_plot_chunk_1.pdf │ │ ├── all_coverage_plot_chunk_2.pdf │ │ ├── all_coverage_plot_chunk_3.pdf │ │ ├── all_coverage_plot_chunk_4.pdf │ │ ├── all_coverage_plot_chunk_5.pdf │ │ ├── all_coverage_plot_chunk_6.pdf │ │ ├── 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