On Protein Problems

• Main Authors: Kuei-Hao Chen, 陳奎昊
• Other Authors: Chia-Tung Lee
• Format: Others
• Language: en_US
• Published: 2003
• Online Access: http://ndltd.ncl.edu.tw/handle/06870427322271521563

碩士 === 國立暨南國際大學 === 資訊工程學系 === 91 === Dr. Beccari discovered first protein in 1747. Since then, protein problems have been widely studied. Since protein applications are more widely used, there will be a lot of problems to be solved. For instance, there are protein folding problem, protein dynamic simulation problem, protein structure alignment problem, protein mapping problem and so on. In the biological point of view, the solutions to these problems usually demand high experimental costs. Therefore, algorithms are needed more effectively to decrease a higher experimental cost. Nowadays, scientists use X-ray diffraction or nuclear magnetic resonance (NMR) to solve the protein problem. Even though chemical experiments can achieve high accuracy, it in the mean time incurs high costs to solve the protein problem. In the area of computer science, most researchers proposed solution methods based upon implicit enumeration. Therefore, our goal is to use an algorithmic approach in computational biology such that the algorithm can have a better time complexity. The theme of this thesis consists of two parts, protein structure alignment problem and protein mapping problem. The protein structure alignment problem is to find the maximum number of match of base pairs between the two given protein structures. An amino acid consists of R group and backbone. We use the nitrogen atom and carbon atom of backbone of amino acid to compare the similarity between two protein structures. The method, based upon dynamic programming approach can find better base pair solutions when all the vectors of nitrogen atoms and carbon atoms between two protein structures are compared. Protein exhibits 3-dimensional structures. The protein mapping problem is to map a protein structure from 3-dimensional space to 2-dimensional space. This problem considers that the overlapping of atoms and the losing of protein structure must be minimal as far as possible because protein function is determined by protein shape. According to our observations, the protein structure without considering R group can be regarded as spanning tree. We use a three-step procedure to solve protein mapping problem. First, we take the atom sequence from a protein structure using minimal spanning tree. Second, we use triangulation method to find all possible mapping point coordinates on the plane. Finally, we use total error method to determine a good solution.