shiyx409 / opencadd

A Python library for structural cheminformatics

OpenCADD

A Python library for structural cheminformatics.

Overview

Some modules of this library are still in early stages of development as indicated below.

• databases.klifs: utilities to query the KLIFS database, offline or online.
• 🚧 io: read and write molecules from/to files.
• 🚧 structure.pocket: identification and analysis of protein (sub)pockets.
• 🚧 structure.superposition (formerly superposer): superimpose macromolecules using sequence and structural information.

Documentation

The documentation is available here.

Citation

If you are using the OpenCADD-KLIFS module, please cite our JOSS publication:

@article{Sydow2022,
  doi = {10.21105/joss.03951},
  url = {https://doi.org/10.21105/joss.03951},
  year = {2022},
  publisher = {The Open Journal},
  volume = {7},
  number = {70},
  pages = {3951},
  author = {Dominique Sydow and Jaime Rodríguez-Guerra and Andrea Volkamer},
  title = {OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database},
  journal = {Journal of Open Source Software}
}

If you are using other modules of the OpenCADD package, please cite our Zenodo entry.

License

opencadd is free software and is licensed under the MIT license. Copyright (c) 2020, Volkamer Lab

Authors

opencadd is the cumulative work of several members of the Volkamer Lab, as well as contributions from students that have participated in our lab. In no particular order:

• Jaime Rodríguez-Guerra, PhD
• Dominique Sydow
• Dennis Köser, Annie Pham, Enes Kurnaz, Julian Pipart (structural superposition, 2020)

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.