Merge pull request #314 from volkamerlab/gg-033-molecular_representat…

…ions [DL Edition] T033: Molecular representations
volkamerlab · Apr 11, 2023 · 005d32a · 005d32a
2 parents 7282212 + 4257582
commit 005d32a
Show file tree

Hide file tree

Showing 15 changed files with 1,772 additions and 0 deletions.
diff --git a/teachopencadd/talktorials/T033_molecular_representations/README.md b/teachopencadd/talktorials/T033_molecular_representations/README.md
@@ -0,0 +1,48 @@
+
+# T033 · Molecular Representations
+
+**Note:** This talktorial is a part of TeachOpenCADD, a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects.
+
+Authors:
+
+- [Gerrit Großmann](https://mosi.uni-saarland.de/people/gerrit/), 2022, Saarland University
+
+
+__Talktorial T033__: This talktorial is part of the TeachOpenCADD pipeline described in the TeachOpenCADD publication (TODO), comprising of talktorials T033 to T038.
+
+
+## Aim of this talktorial
+
+In this talktorial, we conduct the groundwork for the deep learning talkturials.
+Specifically, we learn about molecular representations and find that representing a molecule in a computer is not a trivial task. Differnt representations come with their specific implications and (dis-)advantages.
+
+### Contents in Theory
+
+* What is a molecule?
+* Molecular representations
+* Molecule representations for humans
+* Computer-age molecular representations
+
+
+### Contents in Practical
+
+* Conformers
+* Molecular graphs
+* Fingerprints
+
+
+### References
+
+* Databases: 
+  * [UniProt Protein Database](https://www.uniprot.org/)
+  * [AlphaFold
+Protein Structure Database](https://alphafold.ebi.ac.uk/)
+* Papers: 
+  * [Molecular representations in AI-driven drug discovery: a review and practical guide](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00460-5#:~:text=Traditionally%2C%20molecules%20are%20represented%20as,of%20chemical%20structures%20in%20cheminformatics.)
+  * [A review of molecular representation in the age of machine learning](https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1603)
+  * [Point-based molecular representation learning from conformers](https://openreview.net/pdf?id=pjePBJjlBby)
+* Talkturials: 
+  * [T008 - Protein data acquisition: Protein Data Bank (PDB)](https://github.com/volkamerlab/teachopencadd/blob/master/teachopencadd/talktorials/T008_query_pdb/talktorial.ipynb)
+  * [T017 - Advanced NGLview usage](https://github.com/volkamerlab/teachopencadd/blob/master/teachopencadd/talktorials/T017_advanced_nglview_usage/talktorial.ipynb)
+  * Deep larning talkturials T033 to T038
+* [Tutorial on chirality](https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(Vollhardt_and_Schore)/05._Stereoisomers/5.1%3A_Chiral__Molecules)
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/README.md b/teachopencadd/talktorials/T033_molecular_representations/images/README.md
@@ -0,0 +1,5 @@
+# T033 · Molecular Representations
+
+## Images
+
+This folder stores images used in the Jupyter notebook.
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/butane.png b/teachopencadd/talktorials/T033_molecular_representations/images/butane.png
diff --git a/...cadd/talktorials/T033_molecular_representations/images/butane_and_isobutane.png b/...cadd/talktorials/T033_molecular_representations/images/butane_and_isobutane.png
diff --git a/...ncadd/talktorials/T033_molecular_representations/images/butanol_2enantiomer.png b/...ncadd/talktorials/T033_molecular_representations/images/butanol_2enantiomer.png
diff --git a/...pencadd/talktorials/T033_molecular_representations/images/caffeine_molecule.png b/...pencadd/talktorials/T033_molecular_representations/images/caffeine_molecule.png
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/conformer.png b/teachopencadd/talktorials/T033_molecular_representations/images/conformer.png
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/cpk.png b/teachopencadd/talktorials/T033_molecular_representations/images/cpk.png
diff --git a/...pencadd/talktorials/T033_molecular_representations/images/energy_landscape.jpeg b/...pencadd/talktorials/T033_molecular_representations/images/energy_landscape.jpeg
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/ethanol.png b/teachopencadd/talktorials/T033_molecular_representations/images/ethanol.png
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/graph1_graph2.png b/teachopencadd/talktorials/T033_molecular_representations/images/graph1_graph2.png
diff --git a/teachopencadd/talktorials/T033_molecular_representations/images/isobutane.png b/teachopencadd/talktorials/T033_molecular_representations/images/isobutane.png
diff --git a/...opencadd/talktorials/T033_molecular_representations/images/kinase_inhibitor.png b/...opencadd/talktorials/T033_molecular_representations/images/kinase_inhibitor.png
diff --git a/...cadd/talktorials/T033_molecular_representations/images/ribbon_diagram_tubby.png b/...cadd/talktorials/T033_molecular_representations/images/ribbon_diagram_tubby.png
diff --git a/teachopencadd/talktorials/T033_molecular_representations/talkturial.ipynb b/teachopencadd/talktorials/T033_molecular_representations/talkturial.ipynb