臺灣博碩士論文加值系統

雙硫鍵資料庫包含了4740個已知結構且帶有雙硫鍵的蛋白質 ( 或7880個 protein chains)。 這些蛋白質全部來自於Protein Data Bank 。 依據蛋白質內所含有的雙硫鍵數目， 形成雙硫鍵的cysteins之間連結方式， 以及disulfide patterns， 我們將這些蛋白質分成531 類別。 檢視這些不同的類別， 被歸類在一起的蛋白質， 不管它們的一級序列相似度高或低， 他們的三級結構都是相似的。 因此， 不需要比對整串的序列， 只要輸入蛋白質雙硫鍵的資訊， SSDB便可以找到類似這蛋白質的三級構造。 資料庫的檢索功能包括輸入PDB code， 雙硫鍵的連結方式， 和FASTA格式的胺基酸序列。 為了提供方便檢視搜尋的結果， 我們利用CHIME的軟體來檢視蛋白質的三級結構， 並提供連結到一些作結構分類的資料庫， 如SCOP， CATH and CE。 這些的發現提供的一個新的觀點來看待蛋白質構造與disulfide patterns之間的關係。 對於尋找結構相似的蛋白質亦提供了一個替代的解決途徑。

SSDB is a database that defines a mapping relation from disulfide bond patterns to protein structures. This database contains 4740 disulfide proteins (or 7880 chains) of known structures that contain at least two disulfide bonds. All the disulfide proteins are from Protein Data Bank. The database hierarchically classifies disulfide proteins according to their respective disulfide number, disulfide connectivity and disulfide patterns. There are 531 disulfide-pattern classes, starting from 2 to 19 disulfide bonds. In the database, proteins belonging to each disulfide pattern class correspond to a single fold only, despite possible low sequence identity. This database established a one-to-one mapping relationship from disulfide patterns to folds. Hence, given information of disulfide connectivity, SSDB can find possible folds for sequence of unknown structure without resorting to sequence alignment. SSDB also provides information of basic disulfide patterns common to proteins of similar folds. The database can be queried by using disulfide connectivity, or sequences in FASTA. DSSP also provides the CHIME interface for interactively viewing three-dimensional structures and links to other structural databases such as SCOP, CATH and CE. Our findings shed new light on the relationship between the protein conformations and their disulfide patterns and, and suggest an alternate way of finding structure homologues in homology modeling. The database can be accessed from http://because-1.life.nctu.edu.tw/ssbond.

Abstract 1
中文摘要 2
Content 3
Introduction 5
Database development and administration system overview 8
Materials 9
Methods 10
Step 1:Definitions of disulfide bond numbers 10
Step 2:Definitions of disulfide bond connectivity 10
Step 3:Definitions of disulfide bond pattern 10
Step 4:Definitions of SS ID code 11
Step 5:Definitions of SS tree 12
Step 6:Miorr and analysis CE and SCOP databases 12
World Wide Web interface 13
Uses of the database 13
Submission method in SSDB 13
Query by PDB id code: 13
Query by disulfide bonds number: 14
Query by disulfide bonds connectivity 14
Query by disulfide bond pattern 14
Predict the structure of the protein by similarity disulfide bonds 14
View the disulfide bonds distribution by SS tree 15
Website 16
Results 17
Enumeration of disulfides per sequence (DSN) 17
Enumeration of the disulfide bond connectivity (DSC) 17
Enumeration of the disulfide bond pattern (DSP) 17
Discussions 19
The probability of disulfide bond connectivity (DSC) 19
Useful table: SS Pattern table (DSP) 19
Similar structures, though not necessarily sequence homologues 19
Compare the structure neighborhoods of PDB with SCOP 20
Compare the structure neighborhoods of PDB with CE 21
A overview proof of SSDB by RMSD and ZCEORE values 21
Special structure neighborhood cases in SSDB 22
Conclusions 23
Future application 25
Find out the secret of sub-disulfide bond by a new method - Fuzzy search 25
Maintenance 27
Figure captions 28
Figure 1. 28
Figure 2. 29
Figure 3. 30
Figure 4. 31
Figure 5. 32
Figure 6. 33
Figure 7. 34
Figure 8. 35
Figure 9. 36
Figure 10. 37
Figure 11. 38
Figure 12. 39
Figure 13. 40
Figure 14. 41
Figure 15. 42
Figure 16. 43
Figure 17. 44
Figure 18. 45
Figure 19. 46
Figure 20. 47
Figure 21. 48
Figure 22. 49
Figure 23. 50
Figure 24 . 51
Figure 25 . 52
Tables 53
Table 1. 53
Table 2. 54
Appendices 55
Appendix I 55
Appendix II 61
References 93

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