Day 5- onto the computer simulations

In the Center for BioPhysics, the majority of work is based on computer simulations. Today, with Dimitri, we downloaded our first programs that would allow us to view many protein structures. This program was very interesting because it provides an excellent visual of actual proteins and their resulting structures. Another tool that was used in conjunction with this is the protein data bank. This is located at the website http://rcsb.org/pdb. In order to view the many proteins presented on this site, the Rasmol viewer or another protein viewer is needed. The freeware protein viewer is located at http://openrasmol.org.

In order to best understand these views of the proteins, it is important to understand some basics about proteins. All proteins are comprised of the 20 different amino acids. Of these 20 amino acids, 2 have a negative charge, 2 have a positive charge, 3 are polar, and 13 are nonpolar. These different properties of amino acids are what result in the various protein structures of strands or helices.

This afternoon, we will be attending a series of small mini-workshops on a variety of subjects to see if there are specific topics that would be beneficial to gain more insight on in order to build on our teacher's toolkit. I am looking forward to further training on Geometers sketchpad.