birdday / practical-cheminfromatics-tutorials

Practical Cheminformatics With Open Source Software

A set of Jupyter notebooks for learning Cheminformatics. The links below will open the tutorials on Google Colab.
This way you can run the notebooks without having to install software on your computer. Of course, you can also just clone the repo and run these notebooks on your own computer.

This is a fork of: https://github.com/PatWalters/practical_cheminformatics_tutorials, but I have created a personal copy of the repo so I can actually see things on the contributions graph...

Fundamentals

1. A Whirlwind Introduction to the RDKit for Cheminformatics
2. A Brief Introduction to Pandas for Cheminformatics
3. SMILES Tutorial
4. SMARTS Tutorial
5. Recursive SMARTS - Under Construction
6. Reaction SMARTS - Under Construction

Using datamol and molfeat to Streamline Cheminformatics Workflows

7. Data Manipulation, Descriptors and Clustering

Clustering

8. K-Means Clustering
9. Taylor-Butina Clustering
10. Self-Organizing Maps

Misc Cheminformatics Analysis

11. ChEMBL Ring System Analysis
12. Working With Drug Data from the ChEMBL Database

SAR Analysis

13. Identifying Scaffolds
14. R-group Analysis
15. Positional Analogue Scanning
16. Free-Wilson Analysis
17. Matched Molecular Pairs
18. Matched Molecular Series

Machine Learning Models

19. Build and Test a QSAR Model in 8 Lines of Python
20. Building a Classification Model
21. Comparing Classification Models
22. Building a Regression Model
23. Comparing Regression Models

Additional topics will be added

A Bit of History

These notebooks began as part of a two-day workshop I did at the University of Bonn in 2019. Since then, the notebooks have evolved and additional notebooks have been added. A lot of the notebooks started as posts on my blog, Practical Cheminformatics. I originally had everything running on Binder, but I found some capacity limits with larger groups and moved everything to Google Colab. I'm planning to continue to add to and revise these as long as people are interested.

Suggestions and Corrections Welcome

This is a work in progress. As you can see above, I'm still working on a few of the notebooks. It's more than possible that these tutorials contain mistakes and/or typos. If you find something that should be corrected, please submit an issue or a PR. In addition, I'm always looking to improve the text. Please let me know if there are aspects that could be explained more clearly. I'd also be interested in hearing about additional topics that you'd like to see covered.

Acknowledgements

These tutorials wouldn't be possible without the work of Greg Landrum, Brian Kelley and the RDKit team, as well as Cédric Bouysset and his work on mols2grid. Thanks!