The all-atom protein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates of all atoms on the backbone which includes N, C, and O atoms. In the previous work, we find that the prediction accuracy of the 3D positions of the O atoms is not so good, compared with the other two atoms N and C. Thus, our goal is to refine the positions of the O atoms after the initial prediction of N, C, and O atoms on the backbone has been done by the previous work. Based on the AMBER force field, we modify the energy function to a simplified one with the statistical data on the bond lengths and bond angles of the 21 distinct amino acids (including the nonstandard one). Then, we propose a two-phase refinement method (TPRM) to find the position of each O atom independently that optimizes the modified energy function. We perform our method on two test sets of proteins. The experimental results show that the reconstruction accuracy of our method is better than the previous ones. The solution of our method is also more stable than most of the previous work. Besides, our method runs much faster than the famous prediction tool, SABBAC.
| Identifer | oai:union.ndltd.org:NSYSU/oai:NSYSU:etd-0820108-215243 |
| Date | 20 August 2008 |
| Creators | Chang, Hsiao-Yen |
| Contributors | Shih-Chung Chen, Yow-Ling Shiue, Chang-Biau Yang, Yue-Li Wang, Chia-Ning Yang |
| Publisher | NSYSU |
| Source Sets | NSYSU Electronic Thesis and Dissertation Archive |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0820108-215243 |
| Rights | off_campus_withheld, Copyright information available at source archive |
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