蛋白質結構預測是相當困難的題目，近幾十年來，各式技術和資源的發展幫助我們透過不同的角度來探討這個問題。在這些方法中，從頭計算法(ab initio method)是最直覺的方法，該方法利用物理學原理來模擬蛋白折疊的過程。其他方法則基於尋找同源性的蛋白質，並辨識出最好的三維結構模板(template)來建構蛋白質結構，這些基於模板進行蛋白質結構預測的方法又可分為同源模擬法(homology modeling)和摺疊辨識法(fold recognition)。在此論文中，我們將回顧並討論五個蛋白質結構預測伺服器和四個蛋白質骨幹重建方法所使用的技術與預測成果。

The job of protein structure prediction is not easy. Various types of techniques and resources have been developed and deployed in the past decades to approach this problem from different perspectives. Among these methods, the first and most intuitive one is referred to the ab initio method, which intends to model the protein folding process by means of physical laws. Other methods, such as the comparative modeling methods, are based on the recognition of spatial motifs in protein database. These template-based methods can be further divided into the homology modeling and fold recognition methods. In this thesis, we will review the techniques in the area, in which five protein structure prediction servers and four protein backbone reconstruction methods will be described and surveyed.

THESIS VERIFICATION FORM i
THESIS AUTHORIZATION FORM iii
ACKNOWLEDGEMENT iv
ABSTRACT v
TABLE OF CONTENTS vii
LIST OF FIGURES ix
LIST OF TABLES xii
1 Introduction 1
2 Preliminaries 4
2.1 Proteins 4
2.1.1 Amino Acid Residues 6
2.1.2 Protein Structures 9
2.2 Critical Assessment of Protein Structure Prediction 14
2.3 Evaluation Methods of Structure Prediction 15
2.3.1 Root Mean Square Deviation (RMSD) 16
2.3.2 Global Distance Test-Total Score 17
2.3.3 Template Modeling Score (TM-score) 17
2.4 The Protein Structure Prediction Methodologies 18
2.4.1 Ab Initio Protein Structure Prediction 18
2.4.2 Protein Homology Modeling 20
2.4.3 Protein Treading/Fold Recognition 23
3 A Review of Protein Structure Prediction Methods 25
3.1 Data Formats 25
3.1.1 FASTA Format 25
3.1.2 Protein Data Bank (File Format) 26
3.2 Protein Structure Prediction Methods without Knowing Cα Trace 27
3.2.1 I-TASSER 27
3.2.2 Robetta 29
3.2.3 HHpred 31
3.2.4 RaptorX 35
3.2.5 MULTICOM 38
3.3 Protein Structure Prediction Methods with Cα Trace 41
3.3.1 PULCHRA 42
3.3.2 SABBAC 44
3.3.3 BBQ 46
3.3.4 PD2 ca2main 46
4 Experimental Results 49
5 Conclusions 55
Bibliography 57

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