Protein Backbone Reconstruction with Tool Preference Classification for Standard and Nonstandard Proteins

• Main Authors: Hsin-Fang Wu, 吳欣芳
• Other Authors: Chang-Biau Yang
• Format: Others
• Language: en_US
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/01650908496708950616

碩士 === 國立中山大學 === 資訊工程學系研究所 === 101 === Given a protein sequence and the Cα coordinates on its backbone, the all-atom protein backbone reconstruction problem (PBRP) is to reconstruct the backbone by its 3D coordinates of N, C and O atoms. In the past few decades, many methods have been proposed for solving PBRP, such as ab initio, homology modeling, SABBAC, Wang’s method, Chang’s method, BBQ (Backbone Building from Quadrilaterals) and Chen’s method. Chen found that, if they can choose the correct prediction tool to build the 3D coordinates of the desired atoms, the RMSD may be improved. In this thesis, we propose a method for solving PBRP based on Chen’s method. We use tool preference classification on each atom of the residue, where the classification model is generated by SVM (Support Vector Machine). We rebuild the backbone by combing the prediction results of all atoms in all residues. The data sets used in our experiments are CASP7, CASP8 and CASP9, which have 65, 52 and 63 proteins, respectively. These data sets contain nonstandard amino acids as well as standard ones. We improve the average RMSDs of Chen’s results in some cases. The average RMSDs of our method are 0.3496 in CASP7, 0.3084 in CASP8 and 0.3286 in CASP9.