├── .gitignore ├── LICENSE ├── README.md ├── active_learning ├── active_classification.ipynb ├── active_regression.ipynb ├── active_shape_search.ipynb ├── align3D_score.py ├── data │ ├── 2chw_lig.sdf │ ├── MAPK1.csv │ ├── Mpro_final.csv │ ├── screen.csv │ └── tyk2_fep.csv ├── gen_conformers.py └── images │ └── active_learning.png ├── chemprop ├── data │ └── biogen_logS.csv ├── run_chemprop.ipynb └── run_chemprop_rddesc.ipynb ├── clustering ├── kmeans_clustering.ipynb ├── self_organizing_map.ipynb └── taylor_butina_clustering.ipynb ├── data ├── CHEMBL1075104.smi ├── CHEMBL208.smi ├── CHEMBL313_sel.smi ├── ChEMBL_hERG.csv ├── FEP_vs_GTI-dG-SI.xlsx ├── chembl_herg_log_activity.csv ├── cluster_test.smi ├── dude_erk2_mk01.csv ├── example_compounds.sdf ├── hERG.csv └── smarts_test.smi ├── datamol └── datamol_1.ipynb ├── docking ├── 6g92_ligand.sdf ├── 6g92_protein_fixed.pdb ├── crem_analogs_docked.sdf ├── crem_docked_rmsd_filtered.sdf └── prolif_analysis.ipynb ├── fundamentals ├── A_Whirlwind_Introduction_To_The_RDKit.ipynb ├── SMARTS_tutorial.ipynb ├── SMILES_tutorial.ipynb ├── pandas_intro.ipynb ├── recursive_smarts.ipynb └── stereo_and_tautomers.ipynb ├── generative ├── SMILES_RNN.ipynb └── data │ ├── 2024_08_26_SMILES-RNN_fragment_005_similarity.tar.gz │ └── fragment_005_similarity.json ├── images ├── Niementowski.png ├── Reaction_01A.png ├── Reaction_02A.png ├── Reaction_03.png ├── amide.png ├── smarts_atom_primitives.png ├── smarts_bond_primitives.png └── smarts_tutorial_using_mols2grid.png ├── misc ├── ChEMBL_data_curation.ipynb ├── ChEMBL_hERG_series.ipynb ├── ChEMBL_ring_system_analysis.ipynb ├── substituent_polarity.ipynb ├── visualizing_chemical_space.ipynb └── working_with_ChEMBL_drug_data.ipynb ├── ml_models ├── QSAR_in_8_lines.ipynb ├── classification_model.ipynb ├── comparing_classification_models.ipynb ├── comparing_regression_models.ipynb ├── cross_validation.ipynb └── regression_model.ipynb ├── papers └── ML_FEP │ ├── ML_FEP.ipynb │ └── cSrc_dataset.csv ├── patent ├── data │ └── 35A6EC1A3C9266A38807F72D62C1E3FBki.sdf ├── images │ ├── binding_db_login_1.png │ ├── binding_db_login_2.png │ ├── binding_db_patent_1.png │ ├── binding_db_patent_2.png │ ├── binding_db_patent_download.png │ └── binding_db_patent_search_1.png └── patent_analysis.ipynb ├── pdb ├── binding_db_01.png ├── binding_db_02.png ├── binding_db_03.png ├── binding_db_04.png ├── jupyter_scatter_controls.png ├── monomers_12285.tsv └── pdb_bindingdb_tutorial.ipynb ├── qm └── tautomer_energies.ipynb ├── reaction ├── bayesian_reaction_optimization.ipynb ├── data │ ├── amide_reagents.csv │ ├── direct_arylation.csv │ └── quinazoline_reagents.csv ├── images │ ├── amiderxn_000.png │ ├── amiderxn_001.png │ ├── amiderxn_002.png │ ├── amiderxn_003.png │ ├── amiderxn_004.png │ ├── amiderxn_005.png │ ├── amiderxn_006.png │ ├── amiderxn_007.png │ ├── amiderxn_008.png │ ├── amiderxn_009.png │ ├── amiderxn_010.png │ ├── bayes │ │ ├── Possible_conditions.png │ │ ├── Shields_reaction.png │ │ └── baybe_architecture.png │ ├── quinaz_001.png │ ├── quinaz_002.png │ ├── quinaz_003.png │ ├── quinaz_004.png │ ├── quinaz_005.png │ ├── quinaz_006.png │ ├── quinaz_007.png │ ├── quinaz_008.png │ ├── quinaz_009.png │ ├── quinaz_010.png │ ├── quinaz_011.png │ └── quinaz_012.png ├── reaction_advanced.ipynb └── reaction_basics.ipynb ├── sar_analysis ├── R_group_analysis.ipynb ├── find_scaffolds.ipynb ├── free_wilson.ipynb ├── matched_molecular_pairs.ipynb ├── matched_molecular_series.ipynb ├── positional_analogue_scanning.ipynb └── scaffold_finder.py ├── support_libs ├── bootstrap.py └── delong_ci.py └── tricks_and_tips ├── rdkit_tricks_01.ipynb └── robot_dog.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/README.md -------------------------------------------------------------------------------- /active_learning/active_classification.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/active_classification.ipynb -------------------------------------------------------------------------------- /active_learning/active_regression.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/active_regression.ipynb -------------------------------------------------------------------------------- /active_learning/active_shape_search.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/active_shape_search.ipynb -------------------------------------------------------------------------------- /active_learning/align3D_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/align3D_score.py -------------------------------------------------------------------------------- /active_learning/data/2chw_lig.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/data/2chw_lig.sdf -------------------------------------------------------------------------------- /active_learning/data/MAPK1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/data/MAPK1.csv -------------------------------------------------------------------------------- /active_learning/data/Mpro_final.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/data/Mpro_final.csv -------------------------------------------------------------------------------- /active_learning/data/screen.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/data/screen.csv -------------------------------------------------------------------------------- /active_learning/data/tyk2_fep.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/data/tyk2_fep.csv -------------------------------------------------------------------------------- /active_learning/gen_conformers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/gen_conformers.py -------------------------------------------------------------------------------- /active_learning/images/active_learning.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/active_learning/images/active_learning.png -------------------------------------------------------------------------------- /chemprop/data/biogen_logS.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/chemprop/data/biogen_logS.csv -------------------------------------------------------------------------------- /chemprop/run_chemprop.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/chemprop/run_chemprop.ipynb -------------------------------------------------------------------------------- /chemprop/run_chemprop_rddesc.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/chemprop/run_chemprop_rddesc.ipynb -------------------------------------------------------------------------------- /clustering/kmeans_clustering.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/clustering/kmeans_clustering.ipynb -------------------------------------------------------------------------------- /clustering/self_organizing_map.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/clustering/self_organizing_map.ipynb -------------------------------------------------------------------------------- /clustering/taylor_butina_clustering.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/clustering/taylor_butina_clustering.ipynb -------------------------------------------------------------------------------- /data/CHEMBL1075104.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/CHEMBL1075104.smi -------------------------------------------------------------------------------- /data/CHEMBL208.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/CHEMBL208.smi -------------------------------------------------------------------------------- /data/CHEMBL313_sel.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/CHEMBL313_sel.smi -------------------------------------------------------------------------------- /data/ChEMBL_hERG.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/ChEMBL_hERG.csv -------------------------------------------------------------------------------- /data/FEP_vs_GTI-dG-SI.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/FEP_vs_GTI-dG-SI.xlsx -------------------------------------------------------------------------------- /data/chembl_herg_log_activity.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/chembl_herg_log_activity.csv -------------------------------------------------------------------------------- /data/cluster_test.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/cluster_test.smi -------------------------------------------------------------------------------- /data/dude_erk2_mk01.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/dude_erk2_mk01.csv -------------------------------------------------------------------------------- /data/example_compounds.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/example_compounds.sdf -------------------------------------------------------------------------------- /data/hERG.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/hERG.csv -------------------------------------------------------------------------------- /data/smarts_test.smi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/data/smarts_test.smi -------------------------------------------------------------------------------- /datamol/datamol_1.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/datamol/datamol_1.ipynb -------------------------------------------------------------------------------- /docking/6g92_ligand.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/docking/6g92_ligand.sdf -------------------------------------------------------------------------------- /docking/6g92_protein_fixed.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/docking/6g92_protein_fixed.pdb -------------------------------------------------------------------------------- /docking/crem_analogs_docked.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/docking/crem_analogs_docked.sdf -------------------------------------------------------------------------------- /docking/crem_docked_rmsd_filtered.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/docking/crem_docked_rmsd_filtered.sdf -------------------------------------------------------------------------------- /docking/prolif_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/docking/prolif_analysis.ipynb -------------------------------------------------------------------------------- /fundamentals/A_Whirlwind_Introduction_To_The_RDKit.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/A_Whirlwind_Introduction_To_The_RDKit.ipynb -------------------------------------------------------------------------------- /fundamentals/SMARTS_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/SMARTS_tutorial.ipynb -------------------------------------------------------------------------------- /fundamentals/SMILES_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/SMILES_tutorial.ipynb -------------------------------------------------------------------------------- /fundamentals/pandas_intro.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/pandas_intro.ipynb -------------------------------------------------------------------------------- /fundamentals/recursive_smarts.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/recursive_smarts.ipynb -------------------------------------------------------------------------------- /fundamentals/stereo_and_tautomers.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/fundamentals/stereo_and_tautomers.ipynb -------------------------------------------------------------------------------- /generative/SMILES_RNN.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/generative/SMILES_RNN.ipynb -------------------------------------------------------------------------------- /generative/data/2024_08_26_SMILES-RNN_fragment_005_similarity.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/generative/data/2024_08_26_SMILES-RNN_fragment_005_similarity.tar.gz -------------------------------------------------------------------------------- /generative/data/fragment_005_similarity.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/generative/data/fragment_005_similarity.json -------------------------------------------------------------------------------- /images/Niementowski.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/Niementowski.png -------------------------------------------------------------------------------- /images/Reaction_01A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/Reaction_01A.png -------------------------------------------------------------------------------- /images/Reaction_02A.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/Reaction_02A.png -------------------------------------------------------------------------------- /images/Reaction_03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/Reaction_03.png -------------------------------------------------------------------------------- /images/amide.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/amide.png -------------------------------------------------------------------------------- /images/smarts_atom_primitives.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/smarts_atom_primitives.png -------------------------------------------------------------------------------- /images/smarts_bond_primitives.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/smarts_bond_primitives.png -------------------------------------------------------------------------------- /images/smarts_tutorial_using_mols2grid.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/images/smarts_tutorial_using_mols2grid.png -------------------------------------------------------------------------------- /misc/ChEMBL_data_curation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/ChEMBL_data_curation.ipynb -------------------------------------------------------------------------------- /misc/ChEMBL_hERG_series.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/ChEMBL_hERG_series.ipynb -------------------------------------------------------------------------------- /misc/ChEMBL_ring_system_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/ChEMBL_ring_system_analysis.ipynb -------------------------------------------------------------------------------- /misc/substituent_polarity.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/substituent_polarity.ipynb -------------------------------------------------------------------------------- /misc/visualizing_chemical_space.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/visualizing_chemical_space.ipynb -------------------------------------------------------------------------------- /misc/working_with_ChEMBL_drug_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/misc/working_with_ChEMBL_drug_data.ipynb -------------------------------------------------------------------------------- /ml_models/QSAR_in_8_lines.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/QSAR_in_8_lines.ipynb -------------------------------------------------------------------------------- /ml_models/classification_model.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/classification_model.ipynb -------------------------------------------------------------------------------- /ml_models/comparing_classification_models.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/comparing_classification_models.ipynb -------------------------------------------------------------------------------- /ml_models/comparing_regression_models.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/comparing_regression_models.ipynb -------------------------------------------------------------------------------- /ml_models/cross_validation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/cross_validation.ipynb -------------------------------------------------------------------------------- /ml_models/regression_model.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/ml_models/regression_model.ipynb -------------------------------------------------------------------------------- /papers/ML_FEP/ML_FEP.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/papers/ML_FEP/ML_FEP.ipynb -------------------------------------------------------------------------------- /papers/ML_FEP/cSrc_dataset.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/papers/ML_FEP/cSrc_dataset.csv -------------------------------------------------------------------------------- /patent/data/35A6EC1A3C9266A38807F72D62C1E3FBki.sdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/data/35A6EC1A3C9266A38807F72D62C1E3FBki.sdf -------------------------------------------------------------------------------- /patent/images/binding_db_login_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_login_1.png -------------------------------------------------------------------------------- /patent/images/binding_db_login_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_login_2.png -------------------------------------------------------------------------------- /patent/images/binding_db_patent_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_patent_1.png -------------------------------------------------------------------------------- /patent/images/binding_db_patent_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_patent_2.png -------------------------------------------------------------------------------- /patent/images/binding_db_patent_download.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_patent_download.png -------------------------------------------------------------------------------- /patent/images/binding_db_patent_search_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/images/binding_db_patent_search_1.png -------------------------------------------------------------------------------- /patent/patent_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/patent/patent_analysis.ipynb -------------------------------------------------------------------------------- /pdb/binding_db_01.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/binding_db_01.png -------------------------------------------------------------------------------- /pdb/binding_db_02.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/binding_db_02.png -------------------------------------------------------------------------------- /pdb/binding_db_03.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/binding_db_03.png -------------------------------------------------------------------------------- /pdb/binding_db_04.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/binding_db_04.png -------------------------------------------------------------------------------- /pdb/jupyter_scatter_controls.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/jupyter_scatter_controls.png -------------------------------------------------------------------------------- /pdb/monomers_12285.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/monomers_12285.tsv -------------------------------------------------------------------------------- /pdb/pdb_bindingdb_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/pdb/pdb_bindingdb_tutorial.ipynb -------------------------------------------------------------------------------- /qm/tautomer_energies.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/qm/tautomer_energies.ipynb -------------------------------------------------------------------------------- /reaction/bayesian_reaction_optimization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/bayesian_reaction_optimization.ipynb -------------------------------------------------------------------------------- /reaction/data/amide_reagents.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/data/amide_reagents.csv -------------------------------------------------------------------------------- /reaction/data/direct_arylation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/data/direct_arylation.csv -------------------------------------------------------------------------------- /reaction/data/quinazoline_reagents.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/data/quinazoline_reagents.csv -------------------------------------------------------------------------------- /reaction/images/amiderxn_000.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_000.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_001.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_002.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_002.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_003.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_003.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_004.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_004.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_005.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_005.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_006.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_006.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_007.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_007.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_008.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_008.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_009.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_009.png -------------------------------------------------------------------------------- /reaction/images/amiderxn_010.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/amiderxn_010.png -------------------------------------------------------------------------------- /reaction/images/bayes/Possible_conditions.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/bayes/Possible_conditions.png -------------------------------------------------------------------------------- /reaction/images/bayes/Shields_reaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/bayes/Shields_reaction.png -------------------------------------------------------------------------------- /reaction/images/bayes/baybe_architecture.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/bayes/baybe_architecture.png -------------------------------------------------------------------------------- /reaction/images/quinaz_001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_001.png -------------------------------------------------------------------------------- /reaction/images/quinaz_002.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_002.png -------------------------------------------------------------------------------- /reaction/images/quinaz_003.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_003.png -------------------------------------------------------------------------------- /reaction/images/quinaz_004.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_004.png -------------------------------------------------------------------------------- /reaction/images/quinaz_005.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_005.png -------------------------------------------------------------------------------- /reaction/images/quinaz_006.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_006.png -------------------------------------------------------------------------------- /reaction/images/quinaz_007.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_007.png -------------------------------------------------------------------------------- /reaction/images/quinaz_008.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_008.png -------------------------------------------------------------------------------- /reaction/images/quinaz_009.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_009.png -------------------------------------------------------------------------------- /reaction/images/quinaz_010.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_010.png -------------------------------------------------------------------------------- /reaction/images/quinaz_011.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_011.png -------------------------------------------------------------------------------- /reaction/images/quinaz_012.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/images/quinaz_012.png -------------------------------------------------------------------------------- /reaction/reaction_advanced.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/reaction_advanced.ipynb -------------------------------------------------------------------------------- /reaction/reaction_basics.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/reaction/reaction_basics.ipynb -------------------------------------------------------------------------------- /sar_analysis/R_group_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/R_group_analysis.ipynb -------------------------------------------------------------------------------- /sar_analysis/find_scaffolds.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/find_scaffolds.ipynb -------------------------------------------------------------------------------- /sar_analysis/free_wilson.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/free_wilson.ipynb -------------------------------------------------------------------------------- /sar_analysis/matched_molecular_pairs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/matched_molecular_pairs.ipynb -------------------------------------------------------------------------------- /sar_analysis/matched_molecular_series.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/matched_molecular_series.ipynb -------------------------------------------------------------------------------- /sar_analysis/positional_analogue_scanning.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/positional_analogue_scanning.ipynb -------------------------------------------------------------------------------- /sar_analysis/scaffold_finder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/sar_analysis/scaffold_finder.py -------------------------------------------------------------------------------- /support_libs/bootstrap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/support_libs/bootstrap.py -------------------------------------------------------------------------------- /support_libs/delong_ci.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/support_libs/delong_ci.py -------------------------------------------------------------------------------- /tricks_and_tips/rdkit_tricks_01.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/tricks_and_tips/rdkit_tricks_01.ipynb -------------------------------------------------------------------------------- /tricks_and_tips/robot_dog.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PatWalters/practical_cheminformatics_tutorials/HEAD/tricks_and_tips/robot_dog.png --------------------------------------------------------------------------------