Tutorials

These tutorials provide step-by-step guides for using shepherd-score. They are Jupyter notebooks that you can also download and run interactively.

• Extracting interaction profiles
  • Extract surface
  • Extract electrostatic potential (ESP)
  • Extract pharmacophores
  • Abstracted objects
• Scoring and alignment
  • Convenience classes
  • Raw scoring functions
• Evaluation objects and pipelines
  • Conformer evaluation base class
  • Conformer evaluation pipelines

Tutorial Overview

1. Interaction Profiles (01_profiles.ipynb): Learn how to extract shape, electrostatic, and pharmacophore profiles from molecules.

2. Scoring and Alignment (02_scoring.ipynb): Compute 3D similarity scores and align molecules based on their interaction profiles.

3. Evaluation Pipelines (03_evaluation.ipynb): Use the evaluation framework to assess generated conformers.

Running the Tutorials

To run these tutorials interactively, clone the repository and navigate to the examples/ directory:

git clone https://github.com/coleygroup/shepherd-score.git
cd shepherd-score/examples
jupyter notebook

Make sure you have the required dependencies installed:

pip install "shepherd-score"
pip install jupyter