Packages and webservers used in TeachOpenCADD

TeachOpenCADD uses several external packages and webservers as listed below. If we are using your resource and forgot to add it here, please let us know, thank you!

Python packages

• Cheminformatics and structural bioinformatics:

  • rdkit: http://rdkit.org/

  • openbabel: https://openbabel.org/

  • mdanalysis: https://www.mdanalysis.org/

  • biopython: https://biopython.org/

  • biopandas: https://biopandas.github.io/biopandas/

  • opencadd: https://opencadd.readthedocs.io/en/latest/

  • plip: https://github.com/pharmai/plip

  • openff: https://github.com/openforcefield/openff-toolkit

  • openff-toolkit: https://github.com/openforcefield/openff-toolkit

  • openmmforcefields: https://github.com/openmm/openmmforcefields

  • pdbfixer: https://github.com/openmm/pdbfixer

  • mdanalysis: https://www.mdanalysis.org/

  • biotite: https://www.biotite-python.org/

  • smina: https://sourceforge.net/p/smina/discussion/

• Deep learning:

  • pytorch: https://pytorch.org/

  • pyg: https://pyg.org/

• Data science (PyData stack):

  • numpy: https://numpy.org/

  • pandas: https://pandas.pydata.org/

  • scikit-learn: https://scikit-learn.org/

  • keras: https://keras.io/

  • jupyter: https://jupyter.org/

  • ipywidgets: https://ipywidgets.readthedocs.io

• Data visualization:

  • matplotlib: https://matplotlib.org/

  • mpl_toolkits: https://matplotlib.org/stable/api/toolkits/mplot3d.html

  • matplotlib_venn: https://github.com/konstantint/matplotlib-venn

  • seaborn: https://seaborn.pydata.org/

  • nglview: http://nglviewer.org/nglview/latest/

• Web services clients:

  • pypdb: https://github.com/williamgilpin/pypdb

  • chembl_webresource_client: https://github.com/chembl/chembl_webresource_client

  • requests: https://requests.readthedocs.io/en/latest/

  • bravado: https://bravado.readthedocs.io/en/stable/

  • beautifulsoup4: https://www.crummy.com/software/BeautifulSoup/bs4/doc/

• Utilities:

  • tqdm: https://tqdm.github.io/

  • requests_cache: https://requests-cache.readthedocs.io

  • redo: https://github.com/mozilla-releng/redo

  • google-colab: https://pypi.org/project/google-colab/

  • condacolab: https://pypi.org/project/condacolab/

• Continuous integration:

  • pytest: https://docs.pytest.org

  • nbval: https://nbval.readthedocs.io

• Documentation:

  • sphinx: https://www.sphinx-doc.org

  • nbsphinx: https://nbsphinx.readthedocs.io

• Code style:

  • black-nb: https://github.com/tomcatling/black-nb

Databases and webservers

• ChEMBL: https://www.ebi.ac.uk/chembl/

• RCSB PDB: https://www.rcsb.org/

• KLIFS: https://klifs.net/

• PubMed: https://pubchem.ncbi.nlm.nih.gov/

• ProteinsPlus: https://proteins.plus/