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[1] D. Higgins, & W. Taylor, eds. Bioinformatics:Sequence, Structure and Databanks: A PracticalApproach (Oxford University Press, 2000). [2] D. W. Mount, Bioinformatics: Sequence andGenome Analysis (Cold Spring Harbor Laboratory Press,2004). [3] P. G. Higgs, & T. K. Attwood, Bioinformatics andMolecular Evolution (Wiley-Blackwell 2005). [4] C. L. Worth, & T. L. Blundell, On the evolutionaryconservation of hydrogen bonds made by buried polaramino acids: the hidden joists, braces and trusses ofprotein architecture, BMC Evol Biol, 10, 2010, 161. [5] M. O. Dayhoff, R. M. Schwartz, & B. C. Orcutt, Amodel of evolutionary change in proteins, in Atlas ofProtein Sequence and Structure, M.O. Dayhoff, Editor.1978, National Biomedicinal Research Foundation:Washington, DC. p. 345-352. [6] G. D. Rose, & R. Wolfenden, Hydrogen bonding,hydrophobicity, packing, and protein folding, Annu RevBiophys Biomol Struct, 22, 1993, 381-415. [7] W. A. Baase, A. E. Eriksson, X. J. Zhang, D. W.Heinz, et al., Dissection of protein structure and foldingby directed mutagenesis, Faraday Discuss, (93), 1992,173-81.Figure 6. Alignment of the Glycosyl transferase, family39 signature segment on B4DEA0 to the remaining 16member human proteins591 [8] A. E. Eriksson, W. A. Baase, X. J. Zhang, D. W.Heinz, et al., Response of a protein structure to cavity-creating mutations and its relation to the hydrophobiceffect, Science, 255(5041), 1992, 178-83. [9] H. Cid, M. Bunster, M. Canales, & F. Gazitua,Hydrophobicity and Structural Classes in Proteins,Protein Engineering, 5(5), 1992, 373-375. [10] R. Bhaskaran, & P. K. Ponnuswamy, PositionalFlexibilities of Amino-Acid Residues in Globular-Proteins, International Journal of Peptide and ProteinResearch, 32(4), 1988, 241-255. [11] M. Charton, & B. I. Charton, The StructuralDependence of Amino-Acid Hydrophobicity Parameters,Journal of Theoretical Biology, 99(4), 1982, 629-644. [12] C. Chothia, Nature of Accessible and BuriedSurfaces in Proteins, Journal of Molecular Biology,105(1), 1976, 1-14. [13] C. C. Bigelow, On the average hydrophobicity ofproteins and the relation between it and protein structure,J Theor Biol, 16(2), 1967, 187-211. [14] M. Charton, Protein Folding and the Genetic-Code -an Alternative Quantitative Model, Journal of TheoreticalBiology, 91(1), 1981, 115-123. [15] S. Kawashima, H. Ogata, & M. Kanehisa, AAindex:Amino Acid Index Database, Nucleic Acids Research,27(1), 1999, 368-369. [16] V. S. Mathura, & D. Kolippakkam, APDbase:Amino acid Physico-chemical properties Database,Bioinformation, 1(1), 2005, 2-4. [17] Z. R. Li, H. H. Lin, L. Y. Han, L. Jiang, et al.,PROFEAT: a web server for computing structural andphysicochemical features of proteins and peptides fromamino acid sequence, Nucleic Acids Res. , 34(Web Serverissue), 2006 W32-7. [18] Z. R. Li, H. B. Rao, F. Zhu, G. B. Yang, et al.,Update of PROFEAT: a web server for computingstructural and physicochemical features of proteins andpeptides from amino acid sequence, Nucleic AcidsResearch, 39, 2011, W385-W390. [19] T. L. Bailey, & C. Elkan, Unsupervised Learning ofMultiple Motifs in Biopolymers Using ExpectationMaximization, Machine Learning, 21(1-2), 1995, 51-80. [20] T. L. Bailey, N. Williams, C. Misleh, & W. W. Li,MEME: discovering and analyzing DNA and proteinsequence motifs, Nucleic Acids Research, 34, 2006,W369-W373. [21] S. Balla, V. Thapar, S. Verma, T. Luong, et al.,Minimotif Miner: a tool for investigating protein function,Nat Methods, 3(3), 2006, 175-7. [22] P. Puntervoll, R. Linding, C. Gemund, S. Chabanis-Davidson, et al., ELM server: A new resource forinvestigating short functional sites in modular eukaryoticproteins, Nucleic Acids Res, 31(13), 2003, 3625-30. [23] A. Bairoch, PROSITE: a dictionary of sites andpatterns in proteins, Nucleic Acids Res, 19 Suppl, 1991,2241-5. [24] N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, et al.,The 20 years of PROSITE, Nucleic Acids Res,36(Database issue), 2008, D245-9. [25] N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, et al.,The PROSITE database, Nucleic Acids Res, 34(Databaseissue), 2006, D227-30. [26] L. Y. Geer, M. Domrachev, D. J. Lipman, & S. H.Bryant, CDART: protein homology by domainarchitecture, Genome Res, 12(10), 2002, 1619-23. [27] N. C. Goonesekere, & B. Lee, Context-specificamino acid substitution matrices and their use in thedetection of protein homologs, Proteins, 2007. [28] J. G. Henikoff, S. Pietrokovski, C. M. McCallum, &S. Henikoff, Blocks-based methods for detecting proteinhomology, Electrophoresis, 21(9), 2000, 1700-6. [29] S. Mallat, A Wavelet Tour of Signal Processing(Academic Press, 1998). [30] L. Duret, & S. Abdeddaim, Multiple alignments forstructural, functional, or phylogenetic analysis ofhomologous sequences, in Bioinformatics: Sequence,Structure, and Databanks: A Practical Approach,H.D.a.T. WR, Editor. 2000, Oxford University Press:Oxford. p. 51–76. [31] S. Needleman, & C. Wunsch, A general methodapplicable to the search for similarities in the amino acidsequence of two proteins, Journal of Molecular Biology,48, 1970, 443-453. [32] T. F. Smith, & M. S. Waterman, Identification ofCommon Molecular Subsequences, Journal of MolecularBiology, 147(1), 1981, 195-197. [33] J. G. Henikoff, & S. Henikoff, Blocks database andits applications, Computer Methods for MacromolecularSequence Analysis, 266, 1996, 88-105. [34] I. Daubechies, Ten Lectures on Wavelets (SIAM,1992). [35] R. Apweiler, T. K. Attwood, A. Bairoch, A.Bateman, et al., InterPro - an integrated documentationresource for protein families, domains and functionalsites, Bioinformatics, 16(12), 2000, 1145-1150. [36] S. Hunter, R. Apweiler, T. K. Attwood, A. Bairoch,et al., InterPro: the integrative protein signature database,Nucleic Acids Research, 37, 2009, D211-D215. [37] S. E. Orchard, N. Mulder, & R. Apweiler, TheInterPro database, Molecular & Cellular Proteomics,3(10), 2004, S258-S258. [38] R. D. Finn, J. Mistry, J. Tate, P. Coggill, et al., ThePfam protein families database, Nucleic Acids Res,38(Database issue), 2010, D211-22.
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