Installing Software for Bioinformatics and Cheminformatics

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Old Version of Bioinformatics and Chemoinformatics

  1. Open Anaconda3 and click BioChem001.png
  2. Click create BioChem002.pngand environment titled BioChem37 (You can name the environment whatever you want)
    1. The programming language should be Python 3.7.11
      1. If you did it correctly, it should look like: BioChem003.png
    2. Click the BioChem004.png
    3. Needs to be version 3.7.11 for everything to work.
  3. Click BioChem005.png and click Open Terminal
  4. In terminal and type: conda install -c rdkit rdkit
  5. In terminal type: conda install -c anaconda biopython
  6. In terminal type: conda install -c conda-forge nglview
  7. In terminal type: conda install -c anaconda ipywidgets
  8. Click BioChem006.png
  9. Click BioChem008.png
  10. Getting it to work will take a few minutes. When it is finished the following panel will come up: BioChem009.png
  11. Install Jupyter Notebook while under the BioChem37 environment
  12. 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