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9 Protein Dynamics: From Structure to Function 247Kitao A, Hirata F, Gō N (1991) The effects of solvent on the conformation and the collectivemotions of proteins - normal mode analysis and molecular-dynamics simulations of melittin inwater and vacuum. Chem Phys 158:447–472Kitao A, Hayward S, Gō N (1998) Energy landscape of a native protein: Jumping-among-minimamodel. Proteins 33:496–517Kokubo H, Okamoto Y (2004) Prediction of membrane protein structures by replica-exchangeMonte Carlo simulations: case of two helices. J Chem Phys 120:10837–10847Kubitzki MB, de Groot BL (2007) Molecular dynamics simulations using temperature-enhancedessential dynamics replica exchange. Biophys J 92:4262–4270Kubitzki MB, de Groot BL (2008) The atomistic mechanism of conformational transition in adenylatekinase: a TEE-REX molecular dynamics study. Structure 16:1175–1182Kumar S, Bouzida D, Swendsen RH, et al. (1992) The weighted histogram analysis method forfree-energy calculations on biomolecules. I. the method. J Comp Chem 13:1011–1021Kumar S, Payne PW, Vásquez M (1996) Method for free-energy calculations using iterative techniques.J Comput Chem 17:1269–1275Kuroki R, Weaver LH, Matthews BW (1993) A covalent enzyme-substrate intermediate with saccharidedistortion in a mutant T4 lysozyme. Science 262:2030–2033Levitt M, Sander C, Stern PS (1983) Normal-mode dynamics of a protein: Bovine pancreatictrypsin inhibitor. Int J Quant Chem: Quant Biol Symp 10:181–199Levy RM, Karplus M, Kushick J, et al. (1984a) Evaluation of the configurational entropy forproteins: application to molecular dynamics of an α-helix. Macromolecules17:1370–1374Levy RM, Srinivasan AR, Olsen WK, et al. (1984b) Quasi-harmonic method for studying verylow frequency modes in proteins. Biopolymers 23:1099–1112Liu P, Kim B, Friesner RA, et al. (2005) Replica exchange with solute tempering: A methodfor sampling biological systems in explicit water. Proc Natl Acad Sci USA102:13749–13754Lou H, Cukier RI (2006) Molecular dynamics of apo-adenylate kinase: a distance replicaexchange method for the free energy of conformational fluctuations. J Phys Chem B110:24121–24137Luo R, David L, Gilson ML (2002) Accelerated Poisson-Boltzmann calculations for static anddynamic systems. J Comput Chem 23:1244–1253Lyman E, Zuckerman DM (2006) Ensemble-based convergence analysis of biomolecular trajectories.Biophys J 91:164–172Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored witha plastic network model: adenylate kinase. J Mol Biol 352:807–822Marinari E, Parisi G (1992) Simulated tempering: a new Monte Carlo scheme. Europhys Lett19:451–458Marrink SJ, de Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations.J Phys Chem B 108:750–760Matthews BW, Remington SJ (1974) The three dimensional structure of the lysozyme from bacteriophageT4. Proc Natl Acad Sci USA 71:4178–4182McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature267:585–590Mitsutake A, Sugita Y, Okamoto Y (2001) Generalized-ensemble algorithms for molecular simulationsof biopolymers. Biopolymers 60:96–123Moffat K (2003) The frontiers of time-resolved macromolecular crystallography: movies andchirped X-ray pulses. Faraday Discuss 122:65–77Murata K, Mitsuoka K, Walz T, et al. (2000) Structural determinants of water permeation throughAquaporin-1. Nature 407: 599–605Müller CW, Schulz GE (1992) Structure of the complex between adenylate kinase from Eschericiacoli and the inhibitor Ap 5A refined at 19 Å resolution: a model for a catalytic transition state.J Mol Biol 224:159–177
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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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Page 210 and 211: 8 3D Motifs 203In addition to SITE
Page 212 and 213: 8 3D Motifs 205folds; they shared a
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Page 222 and 223: 8 3D Motifs 215Ivanisenko VA, Pintu
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Page 258 and 259: 252 R.A. LaskowskiConsequently, man
Page 260 and 261: 254 R.A. Laskowskiucla.edu, and Pro
Page 262 and 263: 256 R.A. LaskowskiFig. 10.2 Gene On
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Page 266 and 267: 260 R.A. LaskowskiFig. 10.4 Schemat
Page 268 and 269: 262 R.A. Laskowskiaccessibility and
Page 270 and 271: 264 R.A. LaskowskiFig. 10.6 A ligan
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Page 274 and 275: 268 R.A. LaskowskiFig. 10.8 Example
Page 276 and 277: 270 R.A. LaskowskiReferencesAltschu
Page 278 and 279: 272 R.A. LaskowskiXenarios I, Salwi
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Page 298 and 299: Chapter 12Prediction of Protein Fun
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12 Prediction of Protein Function f
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320 IndexConsensus templates, 205Co
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322 IndexLigand-binding templates,
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324 IndexStructure-function linkage
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