Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/19451
標題: 藉辨認模體來預測水解酶蛋白質之功能
Predicting the function of hydrolase proteins based on the recognition of motifs
作者: 王冠棋
Wang, Kuan-Chi
關鍵字: Protein;模體;motif;function prediction;hydrolase;功能預測;水解酶
出版社: 資訊科學系所
引用: 中文 (1) 圖書 [1] 蔡杰松, “利用蛋白質兩面角辨識α螺旋結構及β摺板結構”, 中興大學資訊科學系, 2006 西文 (1) Books [2] Garrett R.H. and Grisham C. M., Biochemistry, 2nd Ed. New York, 1999 (2) Journal Articles [3] A. Stark, S. Sunyaev and R.B. Russell, (2003) A model for statistical significance of local similarities in structure., Journal of Molecular Biology, 326, 1307-1316. [4] Binkowski TA, Freeman P and Liang J, (2004) pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins, Nucleic Acids Research, 32, W555-W558. [5] Binkowski TA, Naghibzadeh S and Liang J, (2003) CASTp: Computed Atlas of Surface Topography of proteins, Nucleic Acids Research, 31, 3352-3355. [6] Ferre F, Ausiello G, Zanzoni A and Helmer-Citterich M, (2004) SURFACE: a database of protein surface regions for functional annotation, Nucleic Acids Research, 32, D240-D244. [7] Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton JM and Orengo C, (2003) Recognising the fold of a protein structure, Bioinformatics, 19, 1748-1759. [8] Holm L and Sander C, (1993) Protein structure comparison by alignment of distance matrices, Journal of Molecular Biology, 233, 123-138. [9] Ivanisenko VA, Pintus SS, Grigorovich DA and Kolchanov NA, (2004) PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins, Nucleic Acids Research, 32, W549-W554. [10] Jambon M, Imberty A, Deleage G and Geourjon C, (2003) A new bioinformatic approach to detect common 3D sites in protein structures, Proteins: Structure, Function, and Bioinformatics, 52, 137-145. [11] Kleywegt GJ, (1999) Recognition of spatial motifs in protein structures, Journal of Molecular Biology, 285, 1887-1897. [12] Krissinel E and Henrick K, (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica Section D Biological Crystallography, D60, 2256-2268. [13] Laskowski RA, Watson JD and Thornton JM, (2003) from protein structure to biochemical function?, Journal of Structural and Functional Genomics, 4, 167-177. [14] Madej T, Gibrat JF, Bryant SH, (1995) Threading a database of protein cores, Proteins: Structure, Function, and Bioinformatics, 23, 356-369. [15] McGinnis S, Madden TL, (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools, Nucleic Acids Research, 32, W20–W25. [16] Pal D and Eisenberg D, (2005) Inference of protein function from protein structure, Structure, 13,1-10. [17] Porter CT, Bartlett GJ and Thornton JM, (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data, Nucleic Acids Research, 32, D129-D133. [18] Shanahan HP, Garcia MA, Jones S and Thornton JM, (2004) Identifying DNA-binding proteins using structural motifs and the electrostatic potential, Nucleic Acids Research, 32, 4732-4741. [19] Shrager J., (2003) The fiction of function, Bioinformatics, 19, 1934–1936. [20] Soding J., (2004) Protein homology detection by HMM-HMM comparison, Bioinformatics, 21,951-960. [21] Spriggs RV, Artymiuk PJ and Willet P, (2003) Searching for patterns of amino acids in 3D protein structures, Journal of Chemical Information and Computer Sciences, 43, 412-421. [22] The Gene Ontology Consortium, (2000) Gene Ontology: tool for the unification of biology, nature genetics, 25,25-29. [23] Tsuchiya, Y., Kinoshita, K. and Nakamura, H., (2005) PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces, Bioinformatics, 21, 1721-1723. [24] Wangikar PP, Tendulkar AV, Ramya S, Mali DN and Sarawagi S, (2003) Functional sites in protein families uncovered via an objective and automated graph theoretic approach, Journal of Molecular Biology, 326, 955-978. [25] W R Pearson and D J Lipman, (1988) Improved tools for biological sequence comparison, Proceedings of the National Academy of Sciences of the United States of America, 85, 2444–2448. (3) Electronic Resources [26] clustalW http://www.ebi.ac.uk/clustalw/ [27] Enzyme Commission http://www.chem.qmul.ac.uk/iubmb/enzyme/ [28] ExPASy-UniProt Knowledgebase http://www.expasy.org/sprot/ [29] Hidden Markov Model http://www.soe.ucsc.edu/research/compbio/html_format_papers/hughkrogh96/node4.html [30] PRINTS http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/ [31] PROSITE http://www.expasy.org/prosite/ [32] RCSB Protein Data Bank http://www.rcsb.org/pdb/home/home.do
摘要: 
蛋白質在生物體中扮演重要的角色,蛋白質有多種功能例如:運輸、運動、酵素、免疫、支持、保護等功能,而自從人類基因體計畫的完成,蛋白質功能的發現,成為現在重要的工作之一,而蛋白質功能的發現,最正確的方法是屬於使用生物實驗所得到的結果,但是面對龐大數量的蛋白質,使用生物實驗必須消耗大量的金錢與時間,所以配合電腦預測蛋白質功能也成為重要方法之ㄧ,這些方法基本上分成三類,第一種是以序列為基準,第二種是以結構資訊為基準,最後是混合以上兩者,現在有龐大的蛋白質序列資料,大約還有三分之ㄧ沒有發現功能,但是有結構資訊的蛋白質又過少,所以本論文重點放在序列為主的蛋白質功能預測,藉著辨認出蛋白質的模體,判斷出蛋白質的功能,對於水解酶蛋白質之功能的辨識正確率已經達到99%,未來將進行對其他種類的蛋白質進行預測。

Protein plays an important role in organisms. Protein has many kinds of function, for example: transportation, sports, enzymes, immunization, support, protection, etc. After the Human Genome Project had been completed, the discovery of protein function becomes an important work. The method that uses biological experiments can achieve the most accurate results in finding the function of a protein. But lots of money and time are needed to find the functions of so many proteins. Therefore, predicting the function of a protein by computer is an important research issue. The computer methods in predicting protein function can be divided into three classes: methods based on sequences, methods based on structures, and methods that combine the previous two. In this thesis, a method based only on sequences to predict the protein function was proposed. This method predicts functions by recognizing the motifs containied in the sequence. In order to test the proposed method, an experiment has been conducted to predict the seven subfunctions of hydrolase proteins. The accuracy achieved is above 99%.
URI: http://hdl.handle.net/11455/19451
其他識別: U0005-1907200717052100
Appears in Collections:資訊科學與工程學系所

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