The all-atom protein backbone reconstruction problem (PBRP) is to reconstruct the 3D coordinates of all atoms, including N, C, and O atoms on the backbone, for a protein whose primary sequence and £\-carbon coordinates are given. A variety of methods for solving PBRP have been proposed, such as Adcock¡¦s method, SABBAC, BBQ, Chang¡¦s and Yen¡¦s methods. In a recent work, Yen et al. found that the results of Chang¡¦s method are not always better than SABBAC. So they apply a tool preference classification to determine which tool is more suitable for predicting the structure of the given protein. In this thesis, we involve BBQ (Backbone Building from Quadrilaterals) and Chang¡¦s method as our candidate prediction tools. In addition, the tool preferences of different atoms (N, C, O) are determined separately. We call the preference classification as an atom classifier, which is built by support vector machine (SVM). According to the preference classification of each atom classifier, a proper prediction tool, either BBQ or Chang¡¦s method, is used to construct the atom of the target protein. Thus, the combination of all atom results, the backbone structure of a protein is reconstructed. The datasets of our experiments are extracted from CASP7, CASP8, and CASP9, which consists of 30, 24, and 55 proteins, respectively. The proteins of the datasets contain only standard amino acids. We improve the average RMSDs of Yen¡¦s results from 0.4019 to 0.3682 in CASP7, from 0.4543 to 0.4202 in CASP8, and from 0.4155 to 0.3601 in CASP9.
| Identifer | oai:union.ndltd.org:NSYSU/oai:NSYSU:etd-0907111-133928 |
| Date | 07 September 2011 |
| Creators | Chen, Kai-Yu |
| Contributors | Chia-Ning Yang, Kuo-Tsung Tseng, Jen-Sen Lin, Chang-Biau 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-0907111-133928 |
| Rights | user_define, Copyright information available at source archive |
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