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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
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dc.contributor.advisor | 歐陽彥正 | |
dc.contributor.author | Yi-Zhong Weng | en |
dc.contributor.author | 翁翊鍾 | zh_TW |
dc.date.accessioned | 2021-06-13T04:12:37Z | - |
dc.date.available | 2006-08-01 | |
dc.date.copyright | 2006-08-01 | |
dc.date.issued | 2006 | |
dc.date.submitted | 2006-07-24 | |
dc.identifier.citation | 1. Wolfson, H.J.a.R., I., Geometric hashing: an overview. Computational Science and Engineering. IEEE, 1997. 4: p. 10-21.
2. Sayle, R.A. and E.J. Milner-White, RASMOL: biomolecular graphics for all. Trends Biochem Sci, 1995. 20(9): p. 374. 3. Campbell, S.J. and R.M. Jackson, Diversity in the SH2 domain family phosphotyrosyl peptide binding site. Protein Eng, 2003. 16(3): p. 217-27. 4. Zhang, Y. and J. Skolnick, Scoring function for automated assessment of protein structure template quality. Proteins, 2004. 57(4): p. 702-10. 5. Barker, J.A. and J.M. Thornton, An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics, 2003. 19(13): p. 1644-9. 6. Wallace, A.C., N. Borkakoti, and J.M. Thornton, TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci, 1997. 6(11): p. 2308-23. 7. Pearson, W.R., Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol, 1990. 183: p. 63-98. 8. Henikoff, S. and J.G. Henikoff, Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A, 1992. 89(22): p. 10915-9. 9. Berman, H.M., et al., The Protein Data Bank. Nucleic Acids Res, 2000. 28(1): p. 235-42. 10. Laskowski, R.A., PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res, 2001. 29(1): p. 221-2. 11. Porter, C.T., G.J. Bartlett, and J.M. Thornton, The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res, 2004. 32(Database issue): p. D129-33. 12. Altschul, S.F. and E.V. Koonin, Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. Trends Biochem Sci, 1998. 23(11): p. 444-7. 13. Chang D. T.-H. , W.Y.-Z., Lin J.-H., Hwang M.-J., and Oyang Y.-J., Protemot: prediction of protein binding sites with automatically extracted geometrical templates. Nucleic Acids Res, 2006(Webserver issue). 14. Oyang Y.-J., C.D.T.-H., Chen C.-Y. and Hwang S.-C., Expediting Protein Structural Analysis with an Efficient Kernel Density Estimation Algorithm. Proceedings of IEEE 5th International Symposium on Multimedia Software Engineering, Taichung, Taiwan, 2003. 15. Li, W., L. Jaroszewski, and A. Godzik, Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics, 2001. 17(3): p. 282-3. 16. Cormen, T.H., Leiserson C.E., and Rivest, R.L., Introduction to Algorithms. NY: McGraw-Hill, 1990. 17. Janin, J., The targets of CAPRI rounds 3-5. Proteins, 2005. 60(2): p. 170-5. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/32633 | - |
dc.description.abstract | 蛋白質與受質(ligand)之間的結合區域是蛋白質功能的主要作用區域。由於蛋白質的結合區域具有高度的守恆性,使得結合區域可以作為有效辨識蛋白質功能的特殊樣式(motif),所以預測蛋白質結合區域是藥物設計上的一項重要議題。在電腦輔助製藥上,常利用已知的protein-ligand complex分析其立體結構來預測蛋白質與受質之間結合區域;在蛋白質立體結構分析的過程中,如何決定結構的相似度對結果有決定性的影響,所以一直是一個重要的課題。在本論文中,我們利用結合受質周圍的胺基酸作為樣板,針對結合區域的守恆性而進行立體結構分析,以此設計了一套以區域結構分析蛋白質與受質結合區域的程序,並著重在相似度分析的部分。其中比較了現有的相似度評分方式,並提出一個辨識蛋白質種類的新評分方法。我們提出的程序使用在酵素功能預測上,可使預測的準確度從大約40%提升到55%,同時大幅提高預測結果的confidence。這套工具的結果可以提供給生化學家一些有用的線索進行更進一步的研究。 | zh_TW |
dc.description.abstract | The protein-ligand binding site is the major active area of protein function. The property of the volume near protein-ligand binding site is highly correlated to protein function, so the prediction of protein-ligand binding site is a fundamental issue of drug design. Local structure analysis is widely employed in computer aid drug design. How to decide the structural similarity is significance during 3D structure analysis processing. In this thesis, a framework of local structure comparison for prediction of protein-ligand binding site has been proposed. We also provided a comparative analysis of several different scoring functions and designed a novel similarity function on discrimination between homologous protein families. The proposed framework is applied to a functional prediction of enzymes and is able to improve the accuracy from about 40% to 55%. The confidence of the prediction also highly rises. The experimental results provide the biochemists with some valuable clues for in-depth studies. | en |
dc.description.provenance | Made available in DSpace on 2021-06-13T04:12:37Z (GMT). No. of bitstreams: 1 ntu-95-R93922123-1.pdf: 739583 bytes, checksum: 8c7bc1c0fad85189a5cd9282cc413f86 (MD5) Previous issue date: 2006 | en |
dc.description.tableofcontents | CHAPTER 1 導論 1
CHAPTER 2 相關研究 3 2.1 蛋白質結構比對 3 2.2 相似度分析 7 2.3 胺基酸相似性矩陣 11 2.4 蛋白質分類資料庫 14 CHAPTER 3 方法 16 3.1 流程 16 3.2 過濾胺基酸 18 3.3 樣板建構 19 3.4 Geometric Hashing 21 3.5 Refinement 22 3.6 Scoring function 24 CHAPTER 4 實作 32 4.1 樣板建構 32 4.2 Geometric Hashing 36 4.3 Refinement 38 4.4 Constraint 39 CHAPTER 5 實驗 41 5.1 實驗方法 41 5.2 實驗結果 42 Chapter 6 結論 47 參考文獻 49 | |
dc.language.iso | zh-TW | |
dc.title | 利用結構分析預測蛋白質結合區域之研究 | zh_TW |
dc.title | A Study on Using Structural Analysis to Predict Protein Binding Site | en |
dc.type | Thesis | |
dc.date.schoolyear | 94-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 趙坤茂,林榮信,黃乾綱 | |
dc.subject.keyword | 蛋白質,結構分析,結合區域, | zh_TW |
dc.subject.keyword | protein,structural analysis,binding site, | en |
dc.relation.page | 50 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2006-07-26 | |
dc.contributor.author-college | 電機資訊學院 | zh_TW |
dc.contributor.author-dept | 資訊工程學研究所 | zh_TW |
顯示於系所單位: | 資訊工程學系 |
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