Old Version of Bioinformatics and Chemoinformatics

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  1. Open Anaconda3 and create and environment titled Python37 (You can name the environment whatever you want)
    1. The programming language should be Python 3.7
    2. The RDKit Python module does not seem to work on a higher version.
  2. Go to the environment and the terminal and type: conda install -c rdkit rdkit
  3. For Windows 10, go to the environment and type: conda install pywin32
  4. Go to the environment and the terminal and type: conda install -c anaconda spyder=4.21
    1. Does not work on version 5.x yet.
  5. Go to the environment and the terminal and type: conda install spyder-notebook -c spyder-ide
    1. This allows you to run jupyter notebooks within Sypder. See the following.
  6. Open Spyder and type: !pip install chempy
  7. Open Spyder and type: !pip install biopython
  8. Open Spyder and type: !pip install nglview
  9. Open Spyder and type: !pip install ipywidgets
  10. Modules that we are going to explore:
    1. Chemoinformatics
      1. RDKit CookbookPDF
        1. Simplified Molecular Input Line Entry System (SMILES)
        2. PubChem
      2. RDKit Getting Started
      3. RDKit Book
    2. Bioinformatics
      1. Biopython Visualizing and Analyzing ProteinsPDF
        1. Insulin: PDB ID: 4INS
        2. Protein NCBI
        3. Protein Databank Format (PDB)
        4. Common Intermediate Format (CIF)
      2. Biopython ProtParam
      3. Biopython ProtParam Version 2
      4. Biopython Structural Bioinformatics
      5. Biopython Tutorial and Cookbook
      6. Biopython 3D SARS-CoV-2 Protein Visualization With Biopython