參考文獻 |
Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2004. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32, D226-229.
Apweiler, R. et al. 2004. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32, D115-119.
Attwood, T.K., Beck, M.E., Bleasby, A.J., Degtyarenko, K., Michie, A.D., and Parry-Smith, D.J. 1997. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res 25, 212-217.
Bailey, T.L. and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2, 28-36.
Bailey, T.L. and Gribskov, M. 1998. Methods and statistics for combining motif match scores. J Comput Biol 5, 211-221.
Bairoch, A. 1992. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 20, 2013-2018.
Bairoch, A. 1999. The ENZYME data bank in 1999. Nucleic Acids Res 27, 310-311.
Barker, W.C. et al. 2000. The protein information resource (PIR). Nucleic Acids Res 28, 41-44.
Barlow, D.J. and Thornton, J.M. 1983. Ion-pairs in proteins. J Mol Biol 168, 867-885.
Bateman, A. et al. 2004. The Pfam protein families database. Nucleic Acids Res 32, D138-141.
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Wheeler, D.L. 2003. GenBank. Nucleic Acids Res 31, 23-27.
Berman, H.M. et al. 2002. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58, 899-907.
Boeckmann, B. et al. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31, 365-370.
Bolon, D.N. and Mayo, S.L. 2001. Polar residues in the protein core of Escherichia coli thioredoxin are important for fold specificity. Biochemistry 40, 10047-10053.
Branden, C. and Tooze, J. 1991. Introduction to Protein Structure. Garland Publishing Inc.
Burton, S.G. 2003. Oxidizing enzymes as biocatalysts. Trends Biotechnol 21, 543-549.
Chakrabarti, A., Srivastava, S., Swaminathan, C.P., Surolia, A., and Varadarajan, R. 1999. Thermodynamics of replacing an alpha-helical Pro residue in the P40S mutant of Escherichia coli thioredoxin. Protein Sci 8, 2455-2459.
Chakravarty, S. and Varadarajan, R. 2002. Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41, 8152-8161.
Cooper, G. 1989. Current Research Directions in The Development of Expert Systems Based on Belief Networks. Applied Stochastic Models and Data Analysis 5, 39-52.
Corpet, F., Servant, F., Gouzy, J., and Kahn, D. 2000. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res 28, 267-269.
Ding, Y. and Lawrence, C.E. 1999. A bayesian statistical algorithm for RNA secondary structure prediction. Comput Chem 23, 387-400.
Dror, O., Benyamini, H., Nussinov, R., and Wolfson, H. 2003. MASS: multiple structural alignment by secondary structures. Bioinformatics 19, i95-104.
Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press,.
Feinstein, A.R. 1977. Clinical biostatistics. XXXIX. The haze of Bayes, the aerial palaces of decision analysis, and the computerized Ouija board. Clin Pharmacol Ther 21, 482-496.
Frankes, W.B. and Baeza-Yates, R. 1992. Information retrieval: data structures and algorithms. Prentice-Hall, Inc., Upper Saddle River, NJ, USA.
Friedman, N., Linial, M., Nachman, I., and Pe'er, D. 2000. Using Bayesian networks to analyze expression data. J Comput Biol 7, 601-620.
Fukuchi, S. and Nishikawa, K. 2001. Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J Mol Biol 309, 835-843.
Gracia, M.I., Latorre, M.A., Garcia, M., Lazaro, R., and Mateos, G.G. 2003. Heat processing of barley and enzyme supplementation of diets for broilers. Poult Sci 82, 1281-1291.
Gracy, J. and Argos, P. 1998. DOMO: a new database of aligned protein domains. Trends Biochem Sci 23, 495-497.
Gromiha, M.M., Oobatake, M., and Sarai, A. 1999. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys Chem 82, 51-67.
Gromiha, M.M., Uedaira, H., An, J., Selvaraj, S., Prabakaran, P., and Sarai, A. 2002. ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0. Nucleic Acids Res 30, 301-302.
Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714-2723.
Hatzivassiloglou, V., Duboue, P.A., and Rzhetsky, A. 2001. Disambiguating proteins, genes, and RNA in text: a machine learning approach. Bioinformatics 17, S97-106.
Holte, R.C. 1993. Very Simple Classification Rules Perform Well on Most Commonly Used Dataset. In Machine Learning, pp. 63-91.
Horng, J.T., Hu, K.C., Wu, L.C., Huang, H.D., Lin, F.M., Huang, S.L., Lai, H.C., and Chu, T.Y. 2004. Identifying the combination of genetic factors that determine susceptibility to cervical cancer. IEEE Trans Inf Technol Biomed 8, 59-66.
Horng, J.T., Huang, H.D., Wang, S.H., Chen, M.Y., Huang, S.L., and Hwang, J.K. 2003. Computing motif correlations in proteins. J Comput Chem 24, 2032-2043.
Huang, S.L., Wu, L.C., Huang, H.D., Liang, H.K., Ko, M.T., and Horng, J.T. 2004a. A probabilistic method to correlate ion pairs with protein thermostability. Applied Bioinfomatics 3, 21-29.
Huang, S.L., Wu, L.C., Liang, H.K., Pan, K.T., Horng, J.T., and Ko, M.T. 2004b. PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics 20, 276-278.
Jaenicke, R. and Bohm, G. 1998. The stability of proteins in extreme environments. Curr Opin Struct Biol 8, 738-748.
Jaenicke, R. and Bohm, G. 2001. Thermostability of proteins from Thermotoga maritima. Methods Enzymol 334, 438-469.
Jansen, R. et al. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449-453.
Jensen, F. 1996. An Introduction to Bayesian Networks. Springer Verlag, New York.
Kataeva, I.A., Blum, D.L., Li, X.L., and Ljungdahl, L.G. 2001. Do domain interactions of glycosyl hydrolases from Clostridium thermocellum contribute to protein thermostability? Protein Eng 14, 167-172.
Kelley, R.F. and Richards, F.M. 1987. Replacement of proline-76 with alanine eliminates the slowest kinetic phase in thioredoxin folding. Biochemistry 26, 6765-6774.
Klappenbach, J.A., Saxman, P.R., Cole, J.R., and Schmidt, T.M. 2001. rrndb: the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 29, 181-184.
Kreil, D.P. and Ouzounis, C.A. 2001. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 29, 1608-1615.
Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. 1994. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235, 1501-1531.
Kumar, S. and Nussinov, R. 1999. Salt bridge stability in monomeric proteins. J Mol Biol 293, 1241-1255.
Kumar, S. and Nussinov, R. 2001. How do thermophilic proteins deal with heat? Cell Mol Life Sci 58, 1216-1233.
Kumar, S., Tsai, C.J., and Nussinov, R. 2000. Factors enhancing protein thermostability. Protein Eng 13, 179-191.
La, D., Silver, M., Edgar, R.C., and Livesay, D.R. 2003. Using motif-based methods in multiple genome analyses: a case study comparing orthologous mesophilic and thermophilic proteins. Biochemistry 42, 8988-8998.
Ladbury, J.E., Wynn, R., Thomson, J.A., and Sturtevant, J.M. 1995. Substitution of charged residues into the hydrophobic core of Escherichia coli thioredoxin results in a change in heat capacity of the native protein. Biochemistry 34, 2148-2152.
Lebbink, J.H., Knapp, S., van der Oost, J., Rice, D., Ladenstein, R., and de Vos, W.M. 1999. Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface. J Mol Biol 289, 357-369.
Levashov, P., Orlov, V., Boschi-Muller, S., Talfournier, F., Asryants, R., Bulatnikov, I., Muronetz, V., Branlant, G., and Nagradova, N. 1999. Thermal unfolding of phosphorylating D-glyceraldehyde-3-phosphate dehydrogenase studied by differential scanning calorimetry. Biochim Biophys Acta 1433, 294-306.
Lin, T.Y. and Kim, P.S. 1991. Evaluating the effects of a single amino acid substitution on both the native and denatured states of a protein. Proc Natl Acad Sci U S A 88, 10573-10577.
Lubert, S. 1995. Biochemistry. W.H. Freeman Press, New York.
Michael T. Madigan, J.M.M. and Parker, J. 2000. Brock Biology of Microorganisms. Prentice-Hall Inc., New Jersey.
Mitchell, T. 1997. Machine Learning. Mcgraw-Hill Companies, NewYork.
Mulder, N.J. et al. 2003. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 31, 315-318.
Nicastro, G., De Chiara, C., Pedone, E., Tato, M., Rossi, M., and Bartolucci, S. 2000. NMR solution structure of a novel thioredoxin from Bacillus acidocaldarius possible determinants of protein stability. Eur J Biochem 267, 403-413.
Onuchic, J.N., Luthey-Schulten, Z., and Wolynes, P.G. 1997. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 48, 545-600.
Orengo, C.A., Pearl, F.M., and Thornton, J.M. 2003. The CATH domain structure database. Methods Biochem Anal 44, 249-271.
Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444-2448.
Pedone, E., Cannio, R., Saviano, M., Rossi, M., and Bartolucci, S. 1999. Prediction and experimental testing of Bacillus acidocaldarius thioredoxin stability. Biochem J 339, 309-317.
Pedone, E., Saviano, M., Rossi, M., and Bartolucci, S. 2001. A single point mutation (Glu85Arg) increases the stability of the thioredoxin from Escherichia coli. Protein Eng 14, 255-260.
Peter H. A. Sneath, Nicholas S. Mair, Sharpe, M.E., and Holt, J.G. 1986. Bergey's Manual of Systematic Bacteriology. Williams & Wilkins: A Waverly Company.
Qu, K., McCue, L.A., and Lawrence, C.E. 1998. Bayesian protein family classifier. Proc Int Conf Intell Syst Mol Biol 6, 131-139.
Roitel, O., Ivinova, O., Muronetz, V., Nagradova, N., and Branlant, G. 2002. Thermal unfolding used as a probe to characterize the intra- and intersubunit stabilizing interactions in phosphorylating D-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus. Biochemistry 41, 7556-7564.
Servant, F., Bru, C., Carrere, S., Courcelle, E., Gouzy, J., Peyruc, D., and Kahn, D. 2002. ProDom: automated clustering of homologous domains. Brief Bioinform 3, 246-251.
Silverstein, K.A., Shoop, E., Johnson, J.E., and Retzel, E.F. 2001. MetaFam: a unified classification of protein families. I. Overview and statistics. Bioinformatics 17, 249-261.
Szilagyi, A. and Zavodszky, P. 2000. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure Fold Des 8, 493-504.
T.Madigan, M., Martinko, J.M., and Parker, J. 2000. Brock Biology of Microorganisms. Prentice-Hall Inc., New Jersey.
Tatusov, R.L. et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28, 33-36.
Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278, 631-637.
Tatusov, R.L. et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22-28.
Thompson, W., Rouchka, E.C., and Lawrence, C.E. 2003. Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res 31, 3580-3585.
Vieille, C. and Zeikus, G.J. 2001. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65, 1-43.
Vogt, G., Woell, S., and Argos, P. 1997. Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269, 631-643.
Voronov, S., Zueva, N., Orlov, V., Arutyunyan, A., and Kost, O. 2002. Temperature-induced selective death of the C-domain within angiotensin-converting enzyme molecule. FEBS Lett 522, 77-82.
Wackerly, D.D., III, W.M., and Scheaffer, R.L. 1996. Mathematical Statistics with Applications. Duxbury Press, New York.
Wu, C.H., Huang, H., Nikolskaya, A., Hu, Z., and Barker, W.C. 2004. The iProClass integrated database for protein functional analysis. Comput Biol Chem 28, 87-96.
Wu, C.H., Huang, H., Yeh, L.S., and Barker, W.C. 2003. Protein family classification and functional annotation. Comput Biol Chem 27, 37-47.
Wu, C.H., Xiao, C., Hou, Z., Huang, H., and Barker, W.C. 2001. iProClass: an integrated, comprehensive and annotated protein classification database. Nucleic Acids Res 29, 52-54.
Yona, G., Linial, N., and Linial, M. 2000. ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res 28, 49-55.
Zdobnov, E.M. and Apweiler, R. 2001. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848.
Zhu, J., Liu, J.S., and Lawrence, C.E. 1998. Bayesian adaptive sequence alignment algorithms. Bioinformatics 14, 25-39. |