2024-AIDD-人工智能药物设计-使用的软件包和网络服务器

Python 软件包

• 化学信息学和结构生物信息学：
  • 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/
• 深度学习
• pytorch: https://pytorch.org/
• pyg: https://pyg.org/
• 数据科学（PyData 栈）：
  • 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
• 数据可视化：
• 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/
• 网络服务客户：
• 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/
• 公用设施
• 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/
• 持续集成：
• pytest: https://docs.pytest.org
• nbval: https://nbval.readthedocs.io
• 文件：
• sphinx: https://www.sphinx-doc.org
• nbsphinx: https://nbsphinx.readthedocs.io
• 代码样式：
• black-nb: https://github.com/tomcatling/black-nb

数据库和网络服务器

• 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/