2007-2008 Supercomputing Challenge New Mexico Supercomputing Challenge


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Challenge Team Abstract

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    Team Number: 052

    School Name: Albuquerque Academy

    Area of Science: Biological Sciences

    Project Title: Modeling Proteins to determine their tertiary structure

Final Report

Objective: The objective of our project is to create a program that will determine the tertiary structure of the inputed proteins.

Implementation: We will carry out this project by creating a program in C++. This program will have three major modules. The first module is the input module. It will be responsible for user interface. The user will input three letter acronyms that represent the amino acids. These three letters will be processed by the program in its second module. This second module will turn the user's input into a chemical formula. With this formula, it will use the laws of electrostatic attraction to determine its tertiary structure. Tertiary structure, for those biologically inept, is the way a protein folds. Proteins are affected by the polarity of its amino acids because the charge attractions bring two oppositely charged ends closer together. Also, proteins' tertiary structure is affected by covalent or disulfide bridges formed between the sulfur found on methionine and cystine. After the computation module has determined the folding, it will translate its findings into three dimensional coordinates which will then be sent to the third module. This third module, the image module, will produce an image of the folded protein. This image will also distinguish between the different types of atoms, thereby creating a coherent visual representation of the folded protein.

Conclusion: We believe our project will take advantage of the processing power of the supercomputers that we will be using. The advantages of a supercomputer will show up in two areas. The first area is our computational module. The computational model needs to take into account hundreds of variables for each amino acid. Each atom has at least five variables associated with it and each bond has about the same. When you consider that each amino acid group has about twelve to twenty atoms, you begin to realize that a fifteen atom amino group has at least 145 variables associated with it. The supercomputer can calculate the effects of these variables in an acceptable amount of time. The second advantage of a supercomputer is in the image module. The image module needs to have the capability to display our highly complex model, and simple workstations cannot handle this in an acceptable amount of time. We feel that this application of supercomputers will be considered a worthwhile use by future scientists in this field. While our project will most likely no make an impact on the scientific community due to the fact that we are only high school students, we hope that supercomputers will be used in the future for similar applications.

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