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290 J.D. Watson and J.M. ThorntonKim SH, Shin DH, Choi IG, et al. (2003) Structure-based functional inference in structuralgenomics. J Struct Funct Genomics 4:129–135Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast proteinstructure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2256–2268Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state.J Mol Biol 372:774–797Kristensen, DM, Ward RM, Lisewski AM, et al. (2008) Prediction of enzyme function based on3D templates of evolutionarily important amino acids. BMC Bioinformatics 9:17Kuznetsova E, Proudfoot M, Sanders SA, et al. (2005) Enzyme genomics: application of generalenzymatic screens to discover new enzymes. FEMS Microbiol Rev 29:263–279Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, andintermolecular interactions. J Mol Graph 13:323–328Laskowski RA, Watson JD, Thornton JM (2005a) Protein function prediction using local 3D templates.J Mol Biol 351:614–626Laskowski RA, Watson JD, Thornton JM (2005b) ProFunc: a server for predicting protein functionfrom 3D structure. Nucleic Acids Res 33:W89–W93Lecompte O, Ripp R, Thierry JC, et al. (2002) Comparative analysis of ribosomal proteins incomplete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res30:5382–5390Liberles JS, Thaoraolfsson M, Martainez A (2005) Allosteric mechanisms in ACT domain containingenzymes involved in amino acid metabolism. Amino Acids 28:1–12Mons B, Ashburner M, Chichester C, et al. (2008) Calling on a million minds for communityannotation in WikiProteins. Genome Biol 9:R89Noskov VN, Staak K, Shcherbakova PV, et al. (1996) HAM1, the gene controlling 6-N-hydroxylaminopurinesensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Yeast12:17–29Pal D, Eisenberg D (2005) Inference of protein function from protein structure. Structure13:121–130Prilusky J (1996) OCA, a browser-database for protein structure/function. URL http://bip.weizmann.ac.il/ocaand mirrors worldwideProudfoot M, Kuznetsova E, Brown G, et al. (2004) General enzymatic screens identify three newnucleotidases in E. coli: biochemical characterization of SurE, YfbR, and YjjG. J Biol Chem279:54687–54694Rigden DJ (2006) Understanding the cell in terms of structure and function: insights from structuralgenomics. Curr Opin Biotechnol 17:457–464Sanishvili R, Yakunin AF, Laskowski RA, et al. (2003) Integrating structure, bioinformatics, andenzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J BiolChem 278:26039–26045Savchenko A, Krogan N, Cort JR, et al. (2005) The Shwachman-Bodian-Diamond Syndromeprotein family is involved in RNA metabolism. J Biol Chem 280:19213–19220Schade M, Turner CJ, Lowenhaupt K, et al. (1999) Structure-function analysis of the Z-DNAbindingdomain Zalpha of dsRNA adenosine deaminase type I reveals similarity to the (alpha+ beta) family of helix-turn-helix proteins. EMBO J 18:470–479Schroder E, Littlechild JA, Lebedev AA, et al. (2000) Crystal structure of decameric 2-CysPeroxiredoxin from himan erythrocytes at 1.7 Å resolution. Structure 8:605–615Sciara G, Kendrew SG, Miele AE, et al. (2003) The structure of ActVA-Orf6, a novel type ofmonooxygenase involved in actinorhodin biosynthesis. EMBO J 22:205–215Service R (2005) Structural biology. Structural genomics, round 2. Science 307:1554–1558Stark A, Russell RB (2003) Annotation in three dimensions. PINTS: patterns in non-homologoustertiary structures. Nucleic Acids Res 31:3341–3344Stepchenkova EI, Kozmin SG, Alenin VV, et al. (2005) Genome-wide screening for genes whosedeletions confer sensitivity to mutagenic purine base analogs in yeast. BMC Genet 6:31
11 Function Predictions of Structural Genomics Results 291Tan K, Li H, Zhang R, et al. (2008) Structures of open (R) and close (T) states of prephenatedehydratase (PDT) - implication of allosteric regulation by L-phenylalanine. J Struct Biol162:94–107Teichmann SA, Murzin AG, Chothia C (2001) Determination of protein function, evolution andinteractions by structural genomics. Curr Opin Struct Biol 11:354–363Todd A, Orengo C, Thornton JM (2001) Evolution of function in protein superfamilies, from astructural perspective. J Mol Biol 307:1113–1143Watson JD, Sanderson S, Ezersky A, et al. (2007) Towards fully automated structure-based functionprediction in structural genomics: a case study. J Mol Biol 367:1511–1522Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure.Q Rev Biophys 36:307–340Wu R, Skaar EP, Zhang R, et al. (2005) Staphylococcus aureus IsdG and IsdI, heme-degradingenzymes with structural similarity to monooxygenases. J Biol Chem 280:2840–2846Yooseph S, Sutton G, Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition:expanding the universe of protein families. PLoS Biol 5:e16Zhang S, Wilson DB, Ganem B (2000) Probing the catalytic mechanism of prephenate dehydrataseby site-directed mutagenesis of the Escherichia coli P-protein dehydratase domain.Biochemistry 39:4722–4728
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Daniel John RigdenEditorFrom Protei
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ContentsSection I Generating and In
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Contentsxi4.2.1 Alpha-Helical Bundl
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Contentsxiii7.4.2 Predicting Bindin
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Contentsxv12.3 Accuracy and Added V
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4 J. Lee et al.about 5.3 million pr
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6 J. Lee et al.Table 1.1 A list of
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8 J. Lee et al.2000; Sorin and Pand
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10 J. Lee et al.Although most knowl
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12 J. Lee et al.Fig. 1.3 Two exampl
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14 J. Lee et al.rugged containing m
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16 J. Lee et al.1.3.4 Mathematical
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18 J. Lee et al.potentials, each re
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20 J. Lee et al.viewpoint of struct
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22 J. Lee et al.Hsieh MJ, Luo R (20
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24 J. Lee et al.Sippl MJ (1990) Cal
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Chapter 2Fold RecognitionLawrence A
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2 Fold Recognition 29It has long be
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2 Fold Recognition 31Fig. 2.2 Graph
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2 Fold Recognition 33distribute the
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2 Fold Recognition 35Table 2.1 (a)
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2 Fold Recognition 37dependent on t
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2 Fold Recognition 39based on the r
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2 Fold Recognition 41The idea of co
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2 Fold Recognition 43query sequence
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2 Fold Recognition 452.3.4 Consensu
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2 Fold Recognition 472.4 Alignment
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2 Fold Recognition 49statistical me
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2 Fold Recognition 51methods (e.g.
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2 Fold Recognition 53Berman HM, Wes
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2 Fold Recognition 55Tress ML, Jone
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58 A. Fiserwith more than 50% seque
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60 A. FiserIn contrast to ab initio
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62 A. FiserTable 3.1 (continued)SWI
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64 A. Fiserbetween fold recognition
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66 A. FiserFig. 3.1 Comparing accur
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68 A. Fiserinto conserved core regi
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70 A. Fiseralignments are built and
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72 A. Fiserfold, such as the hyperv
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74 A. Fiserfunctions delivers impro
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76 A. Fiserfrom efforts of genome s
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78 A. FiserA rigorous statistical e
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80 A. Fiser(Clore et al. 1993). Cha
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82 A. FiserImproved and new methods
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84 A. FiserClaessens M, Van Cutsem
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86 A. FiserHavel TF, Snow ME (1991)
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88 A. FiserPetrey D, Xiang Z, Tang
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90 A. Fiservan Vlijmen HW, Karplus
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92 T. Nugent and D.T. Jones4.2 Stru
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94 T. Nugent and D.T. JonesFig. 4.2
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96 T. Nugent and D.T. JonesTable 4.
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98 T. Nugent and D.T. Jones2000), d
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100 T. Nugent and D.T. JonesTable 4
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102 T. Nugent and D.T. JonesFig. 4.
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104 T. Nugent and D.T. JonesFig. 4.
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106 T. Nugent and D.T. Jonessubdivi
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108 T. Nugent and D.T. Jonescomplex
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110 T. Nugent and D.T. JonesMartell
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Chapter 5Bioinformatics Approaches
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5 Structure and Function of Intrins
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Chapter 6Function Diversity Within
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6 Function Diversity Within Folds a
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Chapter 7Predicting Protein Functio
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7 Predicting Protein Function from
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Table 7.1 Online resources and tool
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Chapter 83D MotifsElaine C. Meng, B
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8 3D Motifs 189clustering similar s
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8 3D Motifs 191To improve the signa
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8 3D Motifs 193structures together.
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8 3D Motifs 195Table 8.1 (continued
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8 3D Motifs 1978.3.1 User-Defined M
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8 3D Motifs 199Fig. 8.3 The FFF mot
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8 3D Motifs 2018.3.2 Motif Discover
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8 3D Motifs 203In addition to SITE
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8 3D Motifs 205folds; they shared a
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8 3D Motifs 207from a training set
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8 3D Motifs 209Table 8.3 Web server
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8 3D Motifs 211its greater overall
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8 3D Motifs 213Ideally, a 3D motif
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8 3D Motifs 215Ivanisenko VA, Pintu
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Chapter 9Protein Dynamics: From Str
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9 Protein Dynamics: From Structure
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Page 246 and 247: 9 Protein Dynamics: From Structure
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Page 276 and 277: 270 R.A. LaskowskiReferencesAltschu
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Page 324 and 325: 320 IndexConsensus templates, 205Co
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