Team:SJTU-BioX-Shanghai/Protein Atlas
Protein Atlas
Overview
Proteins are the bricks for biological systems. Different proteins have different tertiary structures, therefore they have diverse functions. Some proteins are like barrels, some are spherical, while some are more complex with a combination of multiple parts. If we want to know more about the relationship between protein structure and function, we need to find the structural pattern through all the proteins.
To help a new protein-designer get started quickly, we plan to compose an "atlas of proteins". An atlas is a collection of maps, typically a bundle of maps of Earth or a region of Earth. Here we want to build a collection of protein maps for those famous proteins in biological world.
We want the protein maps to show the not only the protein surface, but the important protein features like shapes, cavities and density distributions. So here, we used different maps to show these characteristics of proteins.
Maps Design
In Protein Atlas, we deigned different kinds of maps for protein.
First of all, we used a animated plot to show the protein surface. In this map, readers can see what this proteins like as their shape.
Besides, we made 3D perspective maps of protein structure. It is marked with protein secondary structure, like alpha-helices and beta-sheets.
Finally, we used a contour map to present the protein structure. Just like terrain map in geography, contour line in terrain maps showed the height, and in protein atlas, contour line showed the same "closeness" to protein center.
Protein Atlas
Reference
[1] Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of computational chemistry, 25(13), 1605-1612.
[2] DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on protein crystallography, 40(1), 82-92.
[3] Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in science & engineering, 9(3), 90-95.
SJTU-BioX-Shanghai
contact us
Contact us: sjtuigem@gmail.com or sjtuigem@gmail.com
Bio-X Institute, Shanghai Jiao Tong University, Dongchuan Rd. 800
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