Our talktorials (portmanteau for talk and tutorial) address many topics central to computer-aided drug design. We have prepared some collections which group our :doc:`extensive list of talktorials <all_talktorials>` into cohesive lessons that deal with one of those topics, including cheminformatic, online queries and structural biology. Enjoy!
Talktorials as presented in the original JCIM 2019 article:
.. nbgallery:: :name: edition2019 talktorials/T001_query_chembl.nblink talktorials/T002_compound_adme.nblink talktorials/T003_compound_unwanted_substructures.nblink talktorials/T004_compound_similarity.nblink talktorials/T005_compound_clustering.nblink talktorials/T006_compound_maximum_common_substructures.nblink talktorials/T007_compound_activity_machine_learning.nblink talktorials/T008_query_pdb.nblink talktorials/T009_compound_ensemble_pharmacophores.nblink talktorials/T010_binding_site_comparison.nblink
Talktorials of the second major release as presented in the Nucleic Acids Research 2022 article:
.. nbgallery:: :name: edition2021 talktorials/T011_query_online_api_webservices.nblink talktorials/T012_query_klifs.nblink talktorials/T013_query_pubchem.nblink talktorials/T014_binding_site_detection.nblink talktorials/T015_protein_ligand_docking.nblink talktorials/T016_protein_ligand_interactions.nblink talktorials/T017_advanced_nglview_usage.nblink talktorials/T018_automated_cadd_pipeline.nblink talktorials/T019_md_simulation.nblink talktorials/T020_md_analysis.nblink talktorials/T021_one_hot_encoding.nblink talktorials/T022_ligand_based_screening_neural_network.nblink
The basis for computer-aided drug discovery
.. nbgallery:: :name: ligandbased talktorials/T001_query_chembl.nblink talktorials/T002_compound_adme.nblink talktorials/T003_compound_unwanted_substructures.nblink talktorials/T004_compound_similarity.nblink talktorials/T005_compound_clustering.nblink talktorials/T006_compound_maximum_common_substructures.nblink talktorials/T007_compound_activity_machine_learning.nblink talktorials/T012_query_klifs.nblink talktorials/T013_query_pubchem.nblink talktorials/T021_one_hot_encoding.nblink talktorials/T022_ligand_based_screening_neural_network.nblink
3D models, structural similarity, protein-ligand interaction analysis and other methods
.. nbgallery:: :name: structuralmodeling talktorials/T008_query_pdb.nblink talktorials/T009_compound_ensemble_pharmacophores.nblink talktorials/T010_binding_site_comparison.nblink talktorials/T012_query_klifs.nblink talktorials/T014_binding_site_detection.nblink talktorials/T015_protein_ligand_docking.nblink talktorials/T016_protein_ligand_interactions.nblink talktorials/T017_advanced_nglview_usage.nblink talktorials/T018_automated_cadd_pipeline.nblink talktorials/T019_md_simulation.nblink talktorials/T020_md_analysis.nblink
Online API/servers for structural bioinformatics and cheminformatics
.. nbgallery:: :name: onlineapi talktorials/T001_query_chembl.nblink talktorials/T008_query_pdb.nblink talktorials/T011_query_online_api_webservices.nblink talktorials/T012_query_klifs.nblink talktorials/T013_query_pubchem.nblink
Kinase similarity comparison using various methods as presented in the LiveCoMS 2021 article:
.. nbgallery:: :name: kinasesimilarity talktorials/T023_what_is_a_kinase.nblink talktorials/T024_kinase_similarity_sequence.nblink talktorials/T025_kinase_similarity_kissim.nblink talktorials/T026_kinase_similarity_ifp.nblink talktorials/T027_kinase_similarity_ligand_profile.nblink talktorials/T028_kinase_similarity_compare_perspectives.nblink
Various deep learning architectures for drug discovery tasks as presented in the ChemRxiv preprint 2023:
.. nbgallery:: :name: deeplearning talktorials/T033_molecular_representations.nblink talktorials/T034_recurrent_neural_networks.nblink talktorials/T035_graph_neural_networks.nblink talktorials/T036_e3_equivariant_gnn.nblink talktorials/T037_uncertainty_estimation.nblink talktorials/T038_protein_ligand_interaction_prediction.nblink