The Protein Structure Series

By | November 28, 2018

Having not added content for a while I think its the right time to start putting together a series of articles centered around my area of expertise, namely Protein Structures.

In this series of articles I will aim to cover some basic essentials about:

  1. Protein Structures.
    • What are they? Why do we need structures? How can we get them and what are some of the most common problems with these structures.
  2. Protein Structure Database.
    • In this we will look at how to get or more structures from the database.
    • What useful information is provided by the database? (The code and data repository will be populated as I go through adding content to this).
  3. Modelling Protein Structures.
    • This article will aim to simply for new users steps necessary to model protein structures when no structure is available.
  4. Protein Structure Analysis.
    • By now you should have an understanding of protein structures. With this article I will provide different scripts that you can use to measure different quantities that can be determined from a protein structure e.g. distance between 2 atoms also called bond length, angles, dihedrals, surface area, solvent accessible surface area etc.
  5. Simulations: Molecular Dynamics and Monte Carlo.
    • With this you should be able to carry out higher levels of analysis with these bio molecules.
    • Analysis of trajectories from simulations will also be discussed.

At present the above list only serves as a guide for me to provide content around. While some of the content here will overlap with previously written articles it will only be reproduced here to help build a context in the discussion.

Furthermore, these articles are planned for my free time which is few and far between. Don’t wait for these articles to come out. If you have a question, write directly to me or have a discussion with me on IDRACK’s Facebook page.

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