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 extensive list of 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:

T001 · Compound data acquisition (ChEMBL)

T002 · Molecular filtering: ADME and lead-likeness criteria

T003 · Molecular filtering: unwanted substructures

T004 · Ligand-based screening: compound similarity

T005 · Compound clustering

T006 · Maximum common substructure

T007 · Ligand-based screening: machine learning

T008 · Protein data acquisition: Protein Data Bank (PDB)

T009 · Ligand-based pharmacophores

T010 · Binding site similarity and off-target prediction

Edition 2021

Talktorials of the second major release as presented in the Nucleic Acids Research 2022 article:

T011 · Querying online API webservices

T012 · Data acquisition from KLIFS

T013 · Data acquisition from PubChem

T014 · Binding site detection

T015 · Protein ligand docking

T016 · Protein-ligand interactions

T017 · Advanced NGLview usage

T018 · Automated pipeline for lead optimization

T019 · Molecular dynamics simulation

T020 · Analyzing molecular dynamics simulations

T021 · One-Hot Encoding

T022 · Ligand-based screening: neural networks

Ligand-based cheminformatics

The basis for computer-aided drug discovery

T001 · Compound data acquisition (ChEMBL)

T002 · Molecular filtering: ADME and lead-likeness criteria

T003 · Molecular filtering: unwanted substructures

T004 · Ligand-based screening: compound similarity

T005 · Compound clustering

T006 · Maximum common substructure

T007 · Ligand-based screening: machine learning

T012 · Data acquisition from KLIFS

T013 · Data acquisition from PubChem

T021 · One-Hot Encoding

T022 · Ligand-based screening: neural networks

Structural biology

3D models, structural similarity, protein-ligand interaction analysis and other methods

T008 · Protein data acquisition: Protein Data Bank (PDB)

T009 · Ligand-based pharmacophores

T010 · Binding site similarity and off-target prediction

T012 · Data acquisition from KLIFS

T014 · Binding site detection

T015 · Protein ligand docking

T016 · Protein-ligand interactions

T017 · Advanced NGLview usage

T018 · Automated pipeline for lead optimization

T019 · Molecular dynamics simulation

T020 · Analyzing molecular dynamics simulations

Online APIs/servers

Online API/servers for structural bioinformatics and cheminformatics

T001 · Compound data acquisition (ChEMBL)

T008 · Protein data acquisition: Protein Data Bank (PDB)

T011 · Querying online API webservices

T012 · Data acquisition from KLIFS

T013 · Data acquisition from PubChem

Kinase similarity

Kinase similarity comparison using various methods as presented in the LiveCoMS 2021 article:

T023 · What is a kinase?

T024 · Kinase similarity: Sequence

T025 · Kinase similarity: Kinase pocket (KiSSim fingerprint)

T026 · Kinase similarity: Interaction fingerprints

T027 · Kinase similarity: Ligand profile

T028 · Kinase similarity: Compare different perspectives

Deep learning

Various deep learning architectures for drug discovery tasks as presented in the ChemRxiv preprint 2023:

T033 · Molecular representations

T034 · RNN-based molecular property prediction

T035 · GNN-based molecular property prediction

T036 · An introduction to E(3)-invariant graph neural networks

T037 · Uncertainty estimation

T038 · Protein Ligand Interaction Prediction