├── .ipynb_checkpoints ├── 1.-Molecular_Docking-checkpoint.ipynb ├── 2.-Virtual_Screening-checkpoint.ipynb ├── 3.-Blind_Docking-checkpoint.ipynb ├── 4.-Reverse_Docking-checkpoint.ipynb └── README-checkpoint.ipynb ├── 1.-Molecular_Docking.ipynb ├── 2.-Virtual_Screening.ipynb ├── 3.-Blind_Docking.ipynb ├── 4.-Reverse_Docking.ipynb ├── 5.- Scaffold_based_Docking.ipynb ├── 6.- Covalent_Docking.ipynb ├── 7.-Docking_Analysis.ipynb ├── Jupyter_Dock.yml ├── LICENSE ├── README.md ├── bin ├── fpocket ├── ledock_linux_x86 ├── ledock_mac ├── lepro_linux_x86 ├── lepro_mac ├── obabel ├── prepare_ligand ├── prepare_receptor ├── qvina-w ├── qvina2.1 ├── smina └── smina.osx ├── img ├── 2d.jpg ├── dock.jpg ├── logo.jpg ├── md.jpg └── pocket.jpg ├── test ├── Blind_Docking │ ├── 1XOZ_clean.pdb │ ├── 1XOZ_clean_H.pdb │ ├── 1XOZ_clean_H_out │ │ ├── pocket10_atm.pdb │ │ ├── pocket10_env_atm.pdb │ │ ├── pocket10_vert.pqr │ │ ├── pocket11_atm.pdb │ │ ├── pocket11_env_atm.pdb │ │ ├── pocket11_vert.pqr │ │ ├── pocket12_atm.pdb │ │ ├── pocket12_env_atm.pdb │ │ ├── pocket12_vert.pqr │ │ ├── pocket13_atm.pdb │ │ ├── pocket13_env_atm.pdb │ │ ├── pocket13_vert.pqr │ │ ├── pocket14_atm.pdb │ │ ├── pocket14_env_atm.pdb │ │ ├── pocket14_vert.pqr │ │ ├── pocket15_atm.pdb │ │ ├── pocket15_env_atm.pdb │ │ ├── pocket15_vert.pqr │ │ ├── pocket16_atm.pdb │ │ ├── pocket16_env_atm.pdb │ │ ├── pocket16_vert.pqr │ │ ├── pocket17_atm.pdb │ │ ├── pocket17_env_atm.pdb │ │ ├── pocket17_vert.pqr │ │ ├── pocket18_atm.pdb │ │ ├── pocket18_env_atm.pdb │ │ ├── pocket18_vert.pqr │ │ ├── pocket19_atm.pdb │ │ ├── pocket19_env_atm.pdb │ │ ├── pocket19_vert.pqr │ │ ├── pocket1_atm.pdb │ │ ├── pocket1_env_atm.pdb │ │ ├── pocket1_vert.pqr │ │ ├── pocket20_atm.pdb │ │ ├── pocket20_env_atm.pdb │ │ ├── pocket20_vert.pqr │ │ ├── pocket21_atm.pdb │ │ ├── pocket21_env_atm.pdb │ │ ├── pocket21_vert.pqr │ │ ├── pocket22_atm.pdb │ │ ├── pocket22_env_atm.pdb │ │ ├── pocket22_vert.pqr │ │ ├── pocket2_atm.pdb │ │ ├── pocket2_env_atm.pdb │ │ ├── pocket2_vert.pqr │ │ ├── pocket3_atm.pdb │ │ ├── pocket3_env_atm.pdb │ │ ├── pocket3_vert.pqr │ │ ├── pocket4_atm.pdb │ │ ├── pocket4_env_atm.pdb │ │ ├── pocket4_vert.pqr │ │ ├── pocket5_atm.pdb │ │ ├── pocket5_env_atm.pdb │ │ ├── pocket5_vert.pqr │ │ ├── pocket6_atm.pdb │ │ ├── pocket6_env_atm.pdb │ │ ├── pocket6_vert.pqr │ │ ├── pocket7_atm.pdb │ │ ├── pocket7_env_atm.pdb │ │ ├── pocket7_vert.pqr │ │ ├── pocket8_atm.pdb │ │ ├── pocket8_env_atm.pdb │ │ ├── pocket8_vert.pqr │ │ ├── pocket9_atm.pdb │ │ ├── pocket9_env_atm.pdb │ │ └── pocket9_vert.pqr │ ├── 1XOZ_lig.mol2 │ ├── 1XOZ_lig_H.mol2 │ ├── 1xoz.pdb1 │ ├── dock.in │ ├── ledock_outfiles │ │ ├── 1XOZ_ledock_pock_1.dok │ │ ├── 1XOZ_ledock_pock_1.sdf │ │ ├── 1XOZ_ledock_pock_10.dok │ │ ├── 1XOZ_ledock_pock_10.sdf │ │ ├── 1XOZ_ledock_pock_11.dok │ │ ├── 1XOZ_ledock_pock_11.sdf │ │ ├── 1XOZ_ledock_pock_12.dok │ │ ├── 1XOZ_ledock_pock_12.sdf │ │ ├── 1XOZ_ledock_pock_13.dok │ │ ├── 1XOZ_ledock_pock_13.sdf │ │ ├── 1XOZ_ledock_pock_14.dok │ │ ├── 1XOZ_ledock_pock_14.sdf │ │ ├── 1XOZ_ledock_pock_15.dok │ │ ├── 1XOZ_ledock_pock_15.sdf │ │ ├── 1XOZ_ledock_pock_16.dok │ │ ├── 1XOZ_ledock_pock_16.sdf │ │ ├── 1XOZ_ledock_pock_17.dok │ │ ├── 1XOZ_ledock_pock_17.sdf │ │ ├── 1XOZ_ledock_pock_18.dok │ │ ├── 1XOZ_ledock_pock_18.sdf │ │ ├── 1XOZ_ledock_pock_19.dok │ │ ├── 1XOZ_ledock_pock_19.sdf │ │ ├── 1XOZ_ledock_pock_2.dok │ │ ├── 1XOZ_ledock_pock_2.sdf │ │ ├── 1XOZ_ledock_pock_20.dok │ │ ├── 1XOZ_ledock_pock_20.sdf │ │ ├── 1XOZ_ledock_pock_21.dok │ │ ├── 1XOZ_ledock_pock_21.sdf │ │ ├── 1XOZ_ledock_pock_22.dok │ │ ├── 1XOZ_ledock_pock_22.sdf │ │ ├── 1XOZ_ledock_pock_3.dok │ │ ├── 1XOZ_ledock_pock_3.sdf │ │ ├── 1XOZ_ledock_pock_4.dok │ │ ├── 1XOZ_ledock_pock_4.sdf │ │ ├── 1XOZ_ledock_pock_5.dok │ │ ├── 1XOZ_ledock_pock_5.sdf │ │ ├── 1XOZ_ledock_pock_6.dok │ │ ├── 1XOZ_ledock_pock_6.sdf │ │ ├── 1XOZ_ledock_pock_7.dok │ │ ├── 1XOZ_ledock_pock_7.sdf │ │ ├── 1XOZ_ledock_pock_8.dok │ │ ├── 1XOZ_ledock_pock_8.sdf │ │ ├── 1XOZ_ledock_pock_9.dok │ │ └── 1XOZ_ledock_pock_9.sdf │ ├── ligand.list │ ├── pocket_descriptors.csv │ ├── smina.log │ └── smina_outfiles │ │ ├── 1XOZ_lig_pocket_1.sdf │ │ ├── 1XOZ_lig_pocket_10.sdf │ │ ├── 1XOZ_lig_pocket_11.sdf │ │ ├── 1XOZ_lig_pocket_12.sdf │ │ ├── 1XOZ_lig_pocket_13.sdf │ │ ├── 1XOZ_lig_pocket_14.sdf │ │ ├── 1XOZ_lig_pocket_15.sdf │ │ ├── 1XOZ_lig_pocket_16.sdf │ │ ├── 1XOZ_lig_pocket_17.sdf │ │ ├── 1XOZ_lig_pocket_18.sdf │ │ ├── 1XOZ_lig_pocket_19.sdf │ │ ├── 1XOZ_lig_pocket_2.sdf │ │ ├── 1XOZ_lig_pocket_20.sdf │ │ ├── 1XOZ_lig_pocket_21.sdf │ │ ├── 1XOZ_lig_pocket_22.sdf │ │ ├── 1XOZ_lig_pocket_3.sdf │ │ ├── 1XOZ_lig_pocket_4.sdf │ │ ├── 1XOZ_lig_pocket_5.sdf │ │ ├── 1XOZ_lig_pocket_6.sdf │ │ ├── 1XOZ_lig_pocket_7.sdf │ │ ├── 1XOZ_lig_pocket_8.sdf │ │ └── 1XOZ_lig_pocket_9.sdf ├── Covalent_Docking │ ├── 6ZRU_clean.pdb │ ├── 6ZRU_clean_H.pdb │ ├── 6zru.pdb1 │ ├── Boce_prep.sdf │ ├── Boceprevir_ref.sdf │ ├── Cov_ScoreFunction.txt │ ├── Smina.sdf │ ├── dock.in │ └── smina.log ├── Molecular_Docking │ ├── 1AZ8_clean.pdb │ ├── 1AZ8_clean_H.pdb │ ├── 1AZ8_clean_H.pdbqt │ ├── 1AZ8_clean_H_fix.pdb │ ├── 1AZ8_lig.mol2 │ ├── 1AZ8_lig_H.dok │ ├── 1AZ8_lig_H.mol2 │ ├── 1AZ8_lig_H.pdbqt │ ├── 1AZ8_lig_ledock_out.sdf │ ├── 1AZ8_lig_smina_out.sdf │ ├── 1AZ8_lig_vina_out.pdbqt │ ├── 1AZ8_lig_vina_out.sdf │ ├── 1az8.pdb1 │ ├── Analysis.sdf │ ├── dock.in │ └── ledock_ligand.list ├── Reverse_Docking │ ├── 2o3p.pdb1 │ ├── 3lm5.pdb1 │ ├── 6m89.pdb1 │ ├── 6qcd.pdb1 │ ├── Quercetin.mol2 │ ├── clean_targets │ │ ├── 2O3P_clean.pdb │ │ ├── 2O3P_clean_H.pdb │ │ ├── 2O3P_clean_H_out │ │ │ ├── pocket10_atm.pdb │ │ │ ├── pocket10_env_atm.pdb │ │ │ ├── pocket10_vert.pqr │ │ │ ├── pocket11_atm.pdb │ │ │ ├── pocket11_env_atm.pdb │ │ │ ├── pocket11_vert.pqr │ │ │ ├── pocket12_atm.pdb │ │ │ ├── pocket12_env_atm.pdb │ │ │ ├── pocket12_vert.pqr │ │ │ ├── pocket13_atm.pdb │ │ │ ├── pocket13_env_atm.pdb │ │ │ ├── pocket13_vert.pqr │ │ │ ├── pocket14_atm.pdb │ │ │ ├── pocket14_env_atm.pdb │ │ │ ├── pocket14_vert.pqr │ │ │ ├── pocket15_atm.pdb │ │ │ ├── pocket15_env_atm.pdb │ │ │ ├── pocket15_vert.pqr │ │ │ ├── pocket16_atm.pdb │ │ │ ├── pocket16_env_atm.pdb │ │ │ ├── pocket16_vert.pqr │ │ │ ├── pocket17_atm.pdb │ │ │ ├── pocket17_env_atm.pdb │ │ │ ├── pocket17_vert.pqr │ │ │ ├── pocket18_atm.pdb │ │ │ ├── pocket18_env_atm.pdb │ │ │ ├── pocket18_vert.pqr │ │ │ ├── pocket19_atm.pdb │ │ │ ├── pocket19_env_atm.pdb │ │ │ ├── pocket19_vert.pqr │ │ │ ├── pocket1_atm.pdb │ │ │ ├── pocket1_env_atm.pdb │ │ │ ├── pocket1_vert.pqr │ │ │ ├── pocket20_atm.pdb │ │ │ ├── pocket20_env_atm.pdb │ │ │ ├── pocket20_vert.pqr │ │ │ ├── pocket2_atm.pdb │ │ │ ├── pocket2_env_atm.pdb │ │ │ ├── pocket2_vert.pqr │ │ │ ├── pocket3_atm.pdb │ │ │ ├── pocket3_env_atm.pdb │ │ │ ├── pocket3_vert.pqr │ │ │ ├── pocket4_atm.pdb │ │ │ ├── pocket4_env_atm.pdb │ │ │ ├── pocket4_vert.pqr │ │ │ ├── pocket5_atm.pdb │ │ │ ├── pocket5_env_atm.pdb │ │ │ ├── pocket5_vert.pqr │ │ │ ├── pocket6_atm.pdb │ │ │ ├── pocket6_env_atm.pdb │ │ │ ├── pocket6_vert.pqr │ │ │ ├── pocket7_atm.pdb │ │ │ ├── pocket7_env_atm.pdb │ │ │ ├── pocket7_vert.pqr │ │ │ ├── pocket8_atm.pdb │ │ │ ├── pocket8_env_atm.pdb │ │ │ ├── pocket8_vert.pqr │ │ │ ├── pocket9_atm.pdb │ │ │ ├── pocket9_env_atm.pdb │ │ │ └── pocket9_vert.pqr │ │ ├── 3LM5_clean.pdb │ │ ├── 3LM5_clean_H.pdb │ │ ├── 3LM5_clean_H_out │ │ │ ├── pocket10_atm.pdb │ │ │ ├── pocket10_env_atm.pdb │ │ │ ├── pocket10_vert.pqr │ │ │ ├── pocket11_atm.pdb │ │ │ ├── pocket11_env_atm.pdb │ │ │ ├── pocket11_vert.pqr │ │ │ ├── pocket12_atm.pdb │ │ │ ├── pocket12_env_atm.pdb │ │ │ ├── pocket12_vert.pqr │ │ │ ├── pocket13_atm.pdb │ │ │ ├── pocket13_env_atm.pdb │ │ │ ├── pocket13_vert.pqr │ │ │ ├── pocket14_atm.pdb │ │ │ ├── pocket14_env_atm.pdb │ │ │ ├── pocket14_vert.pqr │ │ │ ├── pocket15_atm.pdb │ │ │ ├── pocket15_env_atm.pdb │ │ │ ├── pocket15_vert.pqr │ │ │ ├── pocket16_atm.pdb │ │ │ ├── pocket16_env_atm.pdb │ │ │ ├── pocket16_vert.pqr │ │ │ ├── pocket1_atm.pdb │ │ │ ├── pocket1_env_atm.pdb │ │ │ ├── pocket1_vert.pqr │ │ │ ├── pocket2_atm.pdb │ │ │ ├── pocket2_env_atm.pdb │ │ │ ├── pocket2_vert.pqr │ │ │ ├── pocket3_atm.pdb │ │ │ ├── pocket3_env_atm.pdb │ │ │ ├── pocket3_vert.pqr │ │ │ ├── pocket4_atm.pdb │ │ │ ├── pocket4_env_atm.pdb │ │ │ ├── pocket4_vert.pqr │ │ │ ├── pocket5_atm.pdb │ │ │ ├── pocket5_env_atm.pdb │ │ │ ├── pocket5_vert.pqr │ │ │ ├── pocket6_atm.pdb │ │ │ ├── pocket6_env_atm.pdb │ │ │ ├── pocket6_vert.pqr │ │ │ ├── pocket7_atm.pdb │ │ │ ├── pocket7_env_atm.pdb │ │ │ ├── pocket7_vert.pqr │ │ │ ├── pocket8_atm.pdb │ │ │ ├── pocket8_env_atm.pdb │ │ │ ├── pocket8_vert.pqr │ │ │ ├── pocket9_atm.pdb │ │ │ ├── pocket9_env_atm.pdb │ │ │ └── pocket9_vert.pqr │ │ ├── 6M89_clean.pdb │ │ ├── 6M89_clean_H.pdb │ │ ├── 6M89_clean_H_out │ │ │ ├── pocket10_atm.pdb │ │ │ ├── pocket10_env_atm.pdb │ │ │ ├── pocket10_vert.pqr │ │ │ ├── pocket1_atm.pdb │ │ │ ├── pocket1_env_atm.pdb │ │ │ ├── pocket1_vert.pqr │ │ │ ├── pocket2_atm.pdb │ │ │ ├── pocket2_env_atm.pdb │ │ │ ├── pocket2_vert.pqr │ │ │ ├── pocket3_atm.pdb │ │ │ ├── pocket3_env_atm.pdb │ │ │ ├── pocket3_vert.pqr │ │ │ ├── pocket4_atm.pdb │ │ │ ├── pocket4_env_atm.pdb │ │ │ ├── pocket4_vert.pqr │ │ │ ├── pocket5_atm.pdb │ │ │ ├── pocket5_env_atm.pdb │ │ │ ├── pocket5_vert.pqr │ │ │ ├── pocket6_atm.pdb │ │ │ ├── pocket6_env_atm.pdb │ │ │ ├── pocket6_vert.pqr │ │ │ ├── pocket7_atm.pdb │ │ │ ├── pocket7_env_atm.pdb │ │ │ ├── pocket7_vert.pqr │ │ │ ├── pocket8_atm.pdb │ │ │ ├── pocket8_env_atm.pdb │ │ │ ├── pocket8_vert.pqr │ │ │ ├── pocket9_atm.pdb │ │ │ ├── pocket9_env_atm.pdb │ │ │ └── pocket9_vert.pqr │ │ ├── 6QCD_clean.pdb │ │ ├── 6QCD_clean_H.pdb │ │ └── 6QCD_clean_H_out │ │ │ ├── pocket10_atm.pdb │ │ │ ├── pocket10_env_atm.pdb │ │ │ ├── pocket10_vert.pqr │ │ │ ├── pocket11_atm.pdb │ │ │ ├── pocket11_env_atm.pdb │ │ │ ├── pocket11_vert.pqr │ │ │ ├── pocket12_atm.pdb │ │ │ ├── pocket12_env_atm.pdb │ │ │ ├── pocket12_vert.pqr │ │ │ ├── pocket13_atm.pdb │ │ │ ├── pocket13_env_atm.pdb │ │ │ ├── pocket13_vert.pqr │ │ │ ├── pocket14_atm.pdb │ │ │ ├── pocket14_env_atm.pdb │ │ │ ├── pocket14_vert.pqr │ │ │ ├── pocket15_atm.pdb │ │ │ ├── pocket15_env_atm.pdb │ │ │ ├── pocket15_vert.pqr │ │ │ ├── pocket16_atm.pdb │ │ │ ├── pocket16_env_atm.pdb │ │ │ ├── pocket16_vert.pqr │ │ │ ├── pocket17_atm.pdb │ │ │ ├── pocket17_env_atm.pdb │ │ │ ├── pocket17_vert.pqr │ │ │ ├── pocket18_atm.pdb │ │ │ ├── pocket18_env_atm.pdb │ │ │ ├── pocket18_vert.pqr │ │ │ ├── pocket1_atm.pdb │ │ │ ├── pocket1_env_atm.pdb │ │ │ ├── pocket1_vert.pqr │ │ │ ├── pocket2_atm.pdb │ │ │ ├── pocket2_env_atm.pdb │ │ │ ├── pocket2_vert.pqr │ │ │ ├── pocket3_atm.pdb │ │ │ ├── pocket3_env_atm.pdb │ │ │ ├── pocket3_vert.pqr │ │ │ ├── pocket4_atm.pdb │ │ │ ├── pocket4_env_atm.pdb │ │ │ ├── pocket4_vert.pqr │ │ │ ├── pocket5_atm.pdb │ │ │ ├── pocket5_env_atm.pdb │ │ │ ├── pocket5_vert.pqr │ │ │ ├── pocket6_atm.pdb │ │ │ ├── pocket6_env_atm.pdb │ │ │ ├── pocket6_vert.pqr │ │ │ ├── pocket7_atm.pdb │ │ │ ├── pocket7_env_atm.pdb │ │ │ ├── pocket7_vert.pqr │ │ │ ├── pocket8_atm.pdb │ │ │ ├── pocket8_env_atm.pdb │ │ │ ├── pocket8_vert.pqr │ │ │ ├── pocket9_atm.pdb │ │ │ ├── pocket9_env_atm.pdb │ │ │ └── pocket9_vert.pqr │ ├── dock.in │ ├── ledock_outfiles │ │ ├── 2O3P_pock_1.dok │ │ ├── 2O3P_pock_1.sdf │ │ ├── 2O3P_pock_12.dok │ │ ├── 2O3P_pock_12.sdf │ │ ├── 2O3P_pock_13.dok │ │ ├── 2O3P_pock_13.sdf │ │ ├── 2O3P_pock_14.dok │ │ ├── 2O3P_pock_14.sdf │ │ ├── 2O3P_pock_15.dok │ │ ├── 2O3P_pock_15.sdf │ │ ├── 2O3P_pock_16.dok │ │ ├── 2O3P_pock_16.sdf │ │ ├── 2O3P_pock_2.dok │ │ ├── 2O3P_pock_2.sdf │ │ ├── 2O3P_pock_20.dok │ │ ├── 2O3P_pock_20.sdf │ │ ├── 2O3P_pock_3.dok │ │ ├── 2O3P_pock_3.sdf │ │ ├── 2O3P_pock_4.dok │ │ ├── 2O3P_pock_4.sdf │ │ ├── 2O3P_pock_5.dok │ │ ├── 2O3P_pock_5.sdf │ │ ├── 2O3P_pock_6.dok │ │ ├── 2O3P_pock_6.sdf │ │ ├── 2O3P_pock_8.dok │ │ ├── 2O3P_pock_8.sdf │ │ ├── 2O3P_pock_9.dok │ │ ├── 2O3P_pock_9.sdf │ │ ├── 3LM5_pock_1.dok │ │ ├── 3LM5_pock_1.sdf │ │ ├── 3LM5_pock_10.dok │ │ ├── 3LM5_pock_10.sdf │ │ ├── 3LM5_pock_11.dok │ │ ├── 3LM5_pock_11.sdf │ │ ├── 3LM5_pock_15.dok │ │ ├── 3LM5_pock_15.sdf │ │ ├── 3LM5_pock_16.dok │ │ ├── 3LM5_pock_16.sdf │ │ ├── 3LM5_pock_2.dok │ │ ├── 3LM5_pock_2.sdf │ │ ├── 3LM5_pock_4.dok │ │ ├── 3LM5_pock_4.sdf │ │ ├── 3LM5_pock_5.dok │ │ ├── 3LM5_pock_5.sdf │ │ ├── 3LM5_pock_6.dok │ │ ├── 3LM5_pock_6.sdf │ │ ├── 3LM5_pock_7.dok │ │ ├── 3LM5_pock_7.sdf │ │ ├── 3LM5_pock_8.dok │ │ ├── 3LM5_pock_8.sdf │ │ ├── 3LM5_pock_9.dok │ │ ├── 3LM5_pock_9.sdf │ │ ├── 6M89_pock_1.dok │ │ ├── 6M89_pock_1.sdf │ │ ├── 6M89_pock_10.dok │ │ ├── 6M89_pock_10.sdf │ │ ├── 6M89_pock_2.dok │ │ ├── 6M89_pock_2.sdf │ │ ├── 6M89_pock_4.dok │ │ ├── 6M89_pock_4.sdf │ │ ├── 6M89_pock_5.dok │ │ ├── 6M89_pock_5.sdf │ │ ├── 6M89_pock_6.dok │ │ ├── 6M89_pock_6.sdf │ │ ├── 6M89_pock_7.dok │ │ ├── 6M89_pock_7.sdf │ │ ├── 6M89_pock_8.dok │ │ ├── 6M89_pock_8.sdf │ │ ├── 6QCD_pock_1.dok │ │ ├── 6QCD_pock_1.sdf │ │ ├── 6QCD_pock_10.dok │ │ ├── 6QCD_pock_10.sdf │ │ ├── 6QCD_pock_14.dok │ │ ├── 6QCD_pock_14.sdf │ │ ├── 6QCD_pock_15.dok │ │ ├── 6QCD_pock_15.sdf │ │ ├── 6QCD_pock_16.dok │ │ ├── 6QCD_pock_16.sdf │ │ ├── 6QCD_pock_17.dok │ │ ├── 6QCD_pock_17.sdf │ │ ├── 6QCD_pock_18.dok │ │ ├── 6QCD_pock_18.sdf │ │ ├── 6QCD_pock_2.dok │ │ ├── 6QCD_pock_2.sdf │ │ ├── 6QCD_pock_3.dok │ │ ├── 6QCD_pock_3.sdf │ │ ├── 6QCD_pock_4.dok │ │ ├── 6QCD_pock_4.sdf │ │ ├── 6QCD_pock_8.dok │ │ └── 6QCD_pock_8.sdf │ ├── ligand.list │ ├── smina.log │ ├── smina_outfiles │ │ ├── 2O3P_pock_1.sdf │ │ ├── 2O3P_pock_12.sdf │ │ ├── 2O3P_pock_13.sdf │ │ ├── 2O3P_pock_14.sdf │ │ ├── 2O3P_pock_15.sdf │ │ ├── 2O3P_pock_16.sdf │ │ ├── 2O3P_pock_2.sdf │ │ ├── 2O3P_pock_20.sdf │ │ ├── 2O3P_pock_3.sdf │ │ ├── 2O3P_pock_4.sdf │ │ ├── 2O3P_pock_5.sdf │ │ ├── 2O3P_pock_6.sdf │ │ ├── 2O3P_pock_8.sdf │ │ ├── 2O3P_pock_9.sdf │ │ ├── 3LM5_pock_1.sdf │ │ ├── 3LM5_pock_10.sdf │ │ ├── 3LM5_pock_11.sdf │ │ ├── 3LM5_pock_15.sdf │ │ ├── 3LM5_pock_16.sdf │ │ ├── 3LM5_pock_2.sdf │ │ ├── 3LM5_pock_4.sdf │ │ ├── 3LM5_pock_5.sdf │ │ ├── 3LM5_pock_6.sdf │ │ ├── 3LM5_pock_7.sdf │ │ ├── 3LM5_pock_8.sdf │ │ ├── 3LM5_pock_9.sdf │ │ ├── 6M89_pock_1.sdf │ │ ├── 6M89_pock_10.sdf │ │ ├── 6M89_pock_2.sdf │ │ ├── 6M89_pock_4.sdf │ │ ├── 6M89_pock_5.sdf │ │ ├── 6M89_pock_6.sdf │ │ ├── 6M89_pock_7.sdf │ │ ├── 6M89_pock_8.sdf │ │ ├── 6QCD_pock_1.sdf │ │ ├── 6QCD_pock_10.sdf │ │ ├── 6QCD_pock_14.sdf │ │ ├── 6QCD_pock_15.sdf │ │ ├── 6QCD_pock_16.sdf │ │ ├── 6QCD_pock_17.sdf │ │ ├── 6QCD_pock_18.sdf │ │ ├── 6QCD_pock_2.sdf │ │ ├── 6QCD_pock_3.sdf │ │ ├── 6QCD_pock_4.sdf │ │ └── 6QCD_pock_8.sdf │ └── targets_pockets │ │ ├── 2O3P.csv │ │ ├── 3LM5.csv │ │ ├── 6M89.csv │ │ └── 6QCD.csv ├── Scaffold_based_Docking │ ├── 1B38_ATP.sdf │ ├── 1B38_ATP_H.sdf │ ├── 1B38_clean.pdb │ ├── 1B38_clean_H.pdb │ ├── 1b38.pdb1 │ ├── Adenine.sdf │ ├── Cans.sdf │ ├── Confs.sdf │ ├── Smina.sdf │ ├── dock.in │ └── smina.log └── Virtual_Screening │ ├── 1X1R_GDP.mol2 │ ├── 1X1R_clean.pdb │ ├── 1X1R_clean_H.pdb │ ├── 1X1R_lig_smina_out.sdf │ ├── 1x1r.pdb1 │ ├── InputMols.mol2 │ ├── dock.in │ ├── ledock_inputfiles │ ├── mol_0.mol2 │ ├── mol_1.mol2 │ ├── mol_2.mol2 │ ├── mol_3.mol2 │ ├── mol_4.mol2 │ ├── mol_5.mol2 │ ├── mol_6.mol2 │ ├── mol_7.mol2 │ └── mol_8.mol2 │ ├── ledock_outfiles │ ├── mol_0.dok │ ├── mol_0.sdf │ ├── mol_1.dok │ ├── mol_1.sdf │ ├── mol_2.dok │ ├── mol_2.sdf │ ├── mol_3.dok │ ├── mol_3.sdf │ ├── mol_4.dok │ ├── mol_4.sdf │ ├── mol_5.dok │ ├── mol_5.sdf │ ├── mol_6.dok │ ├── mol_6.sdf │ ├── mol_7.dok │ ├── mol_7.sdf │ ├── mol_8.dok │ └── mol_8.sdf │ └── ligand.list └── utilities ├── __pycache__ ├── dok_to_sdf.cpython-37.pyc ├── generate_ledock_file.cpython-37.pyc ├── utils.cpython-37.pyc └── utils.cpython-38.pyc └── utils.py /.ipynb_checkpoints/1.-Molecular_Docking-checkpoint.ipynb: -------------------------------------------------------------------------------- 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