Given an amino acid sequence with the £\-carbon 3D coordinates on its backbone, the all-atom protein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates of all atoms (N, C and O atoms) on the backbone. In this thesis, we propose a method for solving PBRP based on the homology modeling. First, we extract all consecutive 4-residue fragments from all protein structures in PDB. Each fragment is identified by its second, third and fourth residues. Thus, the fragments are classified into 8000 residue groups. In each residue group, the fragments with similar structures are clustered together. And one typical fragment is used to represent one cluster. These typical fragments form our fragment library. Then, we find out possible candidates in the fragment library to reconstruct the backbone of the target protein. To test the performance of our method, we use two testing sets of target proteins, one was proposed by Maupetit et al. [20] and the other is a
subset extracted from CASP7. We compare the experimental results of our method with three previous works MaxSprout, Adcock¡¦s method, and SABBAC proposed by Maupetit et al.. The reconstruction accuracy of our method is comparable to these previous works. And the solution of our method is more stable than the previous works in most target proteins. The time efficiency of our method is also satisfactory.
| Identifer | oai:union.ndltd.org:NSYSU/oai:NSYSU:etd-0828107-231150 |
| Date | 28 August 2007 |
| Creators | Wang, Jen-hui |
| Contributors | Chia-Ning Yang, Chung-Lung Cho, Chang-Biau Yang, Jensen Lin, Yue-Li Wang |
| 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-0828107-231150 |
| Rights | off_campus_withheld, Copyright information available at source archive |
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