https://github.com/rdkit/ugm_2016

Materials from the 2016 RDKit UGM
https://github.com/rdkit/ugm_2016

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Materials from the 2016 RDKit UGM

• Host: GitHub
• URL: https://github.com/rdkit/ugm_2016
• Owner: rdkit
• Created: 2016-10-22T10:04:14.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2017-01-09T08:40:28.000Z (almost 8 years ago)
• Last Synced: 2024-09-26T02:01:34.833Z (3 months ago)
• Language: Jupyter Notebook
• Size: 43.3 MB
• Stars: 38
• Watchers: 14
• Forks: 21
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
# UGM 2016

Materials from the 2016 RDKit UGM in Basel.

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## Lightning Talks

**One central tool for Cheminformatics**

Guillaume Godin

Slides: [Presentations/Godin_OneCentralTool_Lightning.pdf](Presentations/Godin_OneCentralTool_Lightning.pdf)

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**3D pharmacophores in the RDKit**

Nikolaus Stiefl

Notebook: [Notebooks/Stiefl_RDKitPh4FullPublication.ipynb](Notebooks/Stiefl_RDKitPh4FullPublication.ipynb)

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## Presentations / Tutorials

Greg Landrum

State of the toolkit: [Notebooks/State of the toolkit.distrib.ipynb](Notebooks/State of the toolkit.distrib.ipynb)

What's new: [Notebooks/Whats New.ipynb](Notebooks/Whats New.ipynb)

Bonus material, not actually from the UGM:

A brief introduction to the RDKit: [Notebooks/Brief Introduction.ipynb](Notebooks/Brief Introduction.ipynb)

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**An RDKit-centric intro to git and github**

Greg Landrum and Nadine Schneider

Slides: [Presentations/Landrum_Schneider_GitHub_Git_and_RDKit.pdf](Presentations/Landrum_Schneider_GitHub_Git_and_RDKit.pdf)

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**Molecule selectivity prediction for serine proteases**

Simon Ruedisser

Notebook: [Presentations/Ruedisser_SelectivityProteases_talk.ipynb](Presentations/Ruedisser_SelectivityProteases_talk.ipynb)

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**Chemically meaningful ring perception: An open-source implementation of the Unique Ring Families approach**

Florian Flachsenberg

Slides: [Presentations/Flachsenberg_RingDecomposerLib.pdf](Presentations/Flachsenberg_RingDecomposerLib.pdf)

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**Boosting RDKit molecular simulations through OpenMM**

Paolo Tosco

Slides: [Presentations/PaoloTosco_OpenMM_RDKit_integration.pdf](Presentations/PaoloTosco_OpenMM_RDKit_integration.pdf)

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**Data Pipelines and Mol_Lists: RDKit Tools for the Jupyter Notebook**

Axel Pahl

Notebook: [Notebooks/Pahl_NotebookTools_Tutorial.ipynb](Notebooks/Pahl_NotebookTools_Tutorial.ipynb)

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**Matched Molecular Series: Measuring SAR Transferability**

Emanuel Ehmki and Christian Kramer

Slides: [Presentations/Ehmki_and_KramerMatchedMolecularSeries.pdf](Presentations/Ehmki_and_KramerMatchedMolecularSeries.pdf)

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**How to develop RDKit nodes for KNIME workflows**

Manuel Schwarze

Slides: [Presentations/Schwarze_RDKit_UGM_Oct_2016_How_to_Develop_New_RDKit_Nodes.pdf](Presentations/Schwarze_RDKit_UGM_Oct_2016_How_to_Develop_New_RDKit_Nodes.pdf)

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**Five not-so-easy pieces: Tautomers, nucleic acids, inorganics, reactions, and SMIRKS**

Roger Sayle

Slides: [Presentations/Sayle_RDKitTautomers.pdf](Presentations/Sayle_RDKitTautomers.pdf)

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**The origin of three dimensionality in drug-like molecules**

Nathan Brown

Slides: [Presentations/Brown_OriginsOf3D.pdf](Presentations/Brown_OriginsOf3D.pdf)

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**The Novartis Chemical Universe - Searching astronomically large spaces**

Brian Kelley

Slides: [Presentations/BrianKelley-NovartisChemicalUniverse.pdf](Presentations/BrianKelley-NovartisChemicalUniverse.pdf)

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**Higher Quality Chemical Depictions: Lessons Learned and Advice**

John Mayfield

Slides: [Presentations/JohnMayfield_Depiction.pdf](Presentations/JohnMayfield_Depiction.pdf)

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**Faster similarity queries using RDKit, binary fingerprints and relational databases**

Riccardo Vianello

Slides: [Presentations/Vianello_FasterSimilarityQueries.pdf](Presentations/Vianello_FasterSimilarityQueries.pdf)

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**QSAR/ML tutorial**

Nikolas Fechner

Notebooks:

 - [Part 1](Tutorials/Part1_Toy_data_example_and_overfitting_risks.ipynb)

 - [Part 2](Tutorials/Part2_Descriptors_and_regression.ipynb)

 - [Part 3](Tutorials/Part3_Fingerprints_and_classification.ipynb)

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**Implementing RDKit nodes for KNIME**

Manuel Schwarze

Slides: [Presentations/Schwarze_RDKit_UGM_Oct_2016_Workshop_Writing_RDKit_KNIME_Nodes_Hands-On.pdf](Presentations/Schwarze_RDKit_UGM_Oct_2016_Workshop_Writing_RDKit_KNIME_Nodes_Hands-On.pdf)