Molecular Modelling

Molecular modelling is when you use computer software to visualize and manipulate computer representations of real molecules. 

Understanding atoms, molecules, amino acids, and bonding are all really important if you want to become a great biotechnologist! However, often these concepts are hard to understand and visualize because we don't see atoms, molecules and bonds in our everyday lives - they are simply too small! Molecular modelling is a way for you to explore this nano-world world and dive deeper into engineering biology. 

This resource assumes you have read through the Zero to Genetic Engineering Hero Book, especially Chapters 3 and 6, which cover macromolecules and bonding. You may want to refresh these topics by re-reading the chapters as you'll specifically be covering proteins, amino acids, amino acid side chains, CHOPNS, and bonding such as covalent, hydrogen, and VDW.

In the following Free education STEM tutorial that can be done in school or at home, you'll need:

  • A computer
  • Download free open source software PyMOL:
  • Optional (but helpful): a three button mouse 

Molecular Modelling Compilation Part I

The Part I video is a compilation covers a number of different subjects:

  • 00:07: PDB Database Website, Searching Biomolecules, Downloading Files
  • 07:05  Opening PDB files in PyMol, Moving molecules, What you are seeing
  • 16:55  Selecting different things in your molecular model
  • 24:12 Acting upon molecules and basic actions in PyMol
  • 38:14 Measuring between atoms
  • 44:44 Engineering Proteins (Site Directed Mutagenesis at Surface), and Energy Minimization 
  • 55:12 Engineering Proteins (Site Directed Mutagenesis in Protein), and Energy Minimization
  • 1:07:05 Build a Peptide Chain, Adding Hydrogens, Energy Minimization, Save Peptide
  • 1:16:29 Protein Backbone Bond Angles, Ramachandran Plot, Starting Points of your Models


Molecular Modelling Part II

Will build upon Part I and includes more advanced subjects, will be released in early 2021! Follow us on Youtube, so you're the first to know!