NTRK resistance example

With the code and notebooks of this repository we aim to explore the impact of point mutations on ligand binding to NTRKs.

How to use this repository

1. Clone repository

git clone https://github.com/openkinome/ntrk_resistance_example

2. Create Conda environment

conda env create -f environment.yml
conda activate ntrk_mutations

Structure

• data/activities.csv
  • mutational data from Drilon et al. 2017 and Drilon et al. 2018
• notebooks/docking/docking.ipynb
  • jupyter notebook explaining how NTRK structures were prepared and how docking poses were generated
• notebooks/kinoml_modeling/NTRK1_complex_modeling.ipynb
  • jupyter notebook explaining how NTRK structures can automatically be prepared using KinoML
• notebooks/md_sims/md.ipynb
  • jupyter notebook analysing results from MD simulations of systems prepared with docking.

Authors

• David Schaller [email protected]
• William Glass [email protected]

License

This repository is licensed under the MIT license.