Working at a Molecular Level

3D, Just Learning, Molecular, WebGL

The molecular world is a fascinating place. What captivates me is the visuals we accept as a part of the molecular environment tend to be theoretical. This environment is outside of a human’s visual capacity, therefore in order to better understand the form of the chemical compounds we come up with visual mechanisms to understand their structures (of course we use math and very expensive equipment to verify our theories).  After establishing a foundation in chemistry, human understanding of chemical properties led to the capability of visualizing complex chemical structures. A few of the visual mechanisms developed are backbone, ribbon, ball & stick, space-filled and surface models. Through apprehension of structural form, a chemical compound’s functional mechanisms can be better understood.

Image for Chemical Compound Models, via Nick Woolridge

© 2008 Nick Woolridge

This passed Wednesday our class learned how to extract and manipulate files from the Protein Data Bank and use them to visualize chemical models. We explored different methods and programs such as Chimera and mMaya. Another program we did not go over, but worth exploring, is BioBlender.

The model I have decided to play with is the human growth hormone (GH). This hormone is manufactured in the anterior pituitary gland, then released into the blood stream where it then travels to the liver. In the liver GH stimulates the production of  insulin-like growth factor 1 (IGF-1). IGF-1 then leads to the growth of long bones as well as facilitate growth of muscle cells.

After extracting the data from the Protein Data Bank website, I slightly modified the surface model in Chimera. I played around with the colors of the different chemicals, and tried to understand how each molecule was broken down. Sometimes the protein can be divided into different chains.

Link to WebGL - Human GH Surface Model

Link to WebGL - Human GH Ribbon Model

My next step is to use take the extracted PDB file and display the molecule in a 3D environment. Stay tuned for sweet visualizations ahead!


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