Talktorials by collection
=========================

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!

Edition 2019 - JCIM
-------------------

Talktorials as presented in the original `JCIM 2019 article <https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x>`_:

.. 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

Edition 2021
------------

Talktorials of the second major release as presented in the `Nucleic Acids Research 2022 article <https://academic.oup.com/nar/article/50/W1/W753/6582172>`_:

.. 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


Ligand-based cheminformatics
----------------------------

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

Structural biology
------------------

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 APIs/servers
-------------------

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
-------------------

Kinase similarity comparison using various methods as presented in the `LiveCoMS 2021 article <https://doi.org/10.33011/livecoms.3.1.1599>`_:

.. 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


Deep learning 
-------------------

Various deep learning architectures for drug discovery tasks as presented in the `ChemRxiv preprint 2023 <https://doi.org/10.26434/chemrxiv-2023-kz1pb>`_:

.. 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