Code snippets from Team-SKI

This repository contains code snippets that shall demonstrate the use of RDKit, pandas, and other python libaries for common computer-aided drug design tasks.

├── Cheminformatics
│   └── scaffold-analysis
│
├── Kinase inhibitors
│   └── approved-or-in-clinical-trials
│
├── Presentations and Tutorials
│   ├── Molecular Modelling Workshop 2014
│   └── Protvec demo 2017
│   └── RDKit UGM 2014
│       └── hackaton
│
└── Virtual-Screening

These projects were supported by BioMed X Innovation Center, Heidelberg

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Presentations and tutorials

• Molecular Modelling Workshop 2014
  Scaffold analysis in Python with RDKit and pandas
  Jupyter notebook: view

• Protvec demo 2017
  Demo of encoding protein sequences via vectors

• RDKit UGM 2014 - RDKit UGM
  Scaffold analysis of ChEMBL data with pandas and RDKit
  Jupyter notebook: view

  hackaton contribution
  Demo of SaveXlsxFromFrame function that can export PandasDataFrame to Excel including images of molecules.
  Jupyter notebook: view -- Resulting demo xlsx: download

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Cheminformatics

• Scaffold analysis in Python with RDKit and pandas
  Internal presentation given at BioMed X team meeting, March 2014.
  Jupyter notebook: view

• Markdown usage
  Jupyter notebook: view

• RDKit pandas integration
  Demo of new functions that were integrated in [RDKit] (https://github.com/rdkit/rdkit/commit/8269bc9002cf3c6b106c847d86bcbabc016b697e), 2013.
  Jupyter notebook: view

• Rendering of images in IPython
  Example of how to use object representations.
  Jupyter notebook: view

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Kinase-Inhibitors

• approved or in clinical trials
  Notebook that extracts all kinase inhibitors that are in clinical trials or are on the market.
  Jupyter notebook: view

---

Virtual-Screening

• ligand-3D-conformations
  prepare_for_docking.py: Script that uses Open Babel to generate 3D structures of compounds.
  For usage info run prepare_for_docking.py -h

• filtering
  filter_pains.py: Script that uses RDKit to remove PAINS compounds from sdf or smile files.
  For usage info run filter_pains.py -h