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9 Protein Dynamics: From Structure to Function 245Bartels C, Karplus M (1998) Probability distributions for complex systems: Adaptive umbrellasampling of the potential energy. J Phys Chem B 102:865–880Berendsen HJC, Postma JPM, di Nola A, et al. (1984) Molecular dynamics with coupling to anexternal bath. J Chem Phys 81:3684–3690Berg BA, Celik T (1992) New approach to spin-glass simulations. Phys Rev Lett 69:2292–2295Berg BA, Neuhaus T (1991) Multicanonical algorithms for first-order phase transitions. Phys Lett267:249–253Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry, fifth edition. WH Freeman, New YorkBond PJ, Holyoake J, Ivetac A, et al. (2007) Coarse-grained molecular dynamics simulations ofmembrane proteins and peptides. J Struct Biol 157:593–605Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations inbovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 80:6571–6575Brooks BR, Bruccoleri RE, Olafson BD, et al. (1983) CHARMM: a program for macromolecularenergy minimization and dynamics calculations. J Comp Chem 4:187–217Burykin A, Warshel A (2003) What really prevents proton transport through aquaporin? Chargeself-energy versus proton wire proposals. Biophys J 85:3696–3706Cecchini M, Rao F, Seeber M, et al. (2004) Replica exchange molecular dynamics simulations ofamyloid peptide aggregation. J Chem Phys 121:10748–10756Chakrabarti N, Tajkhorshid E, Roux B, et al. (2004) Molecular basis of proton blockage inaquaporins. Structure 12:65–74Chen H, Wu Y, Voth GA (2006) Origins of proton transport behavior from selectivity domainmutations of the aquaporin-1 channel. Biophys J 90:L73–L75Cheng X, Cui G, Hornak V, et al. (2005) Modified replica exchange simulation for local structurerefinement. J Phys Chem B 109:8220–8230Chodera JD, Swope WC, Pitera JW, et al. (2007) Use of the weighted histogram analysis methodfor the analysis of simulated and parallel tempering simulations. J Chem Theory Comput3:26–41Christen M, van Gunsteren WF (2006) Multigraining: an algorithm for simultaneous fine-grainedand coarse-grained simulation of molecular systems. J Chem Phys 124:154106Cook A, Fernandez E, Lindner D, et al. (2005) The structure of the nuclear export receptor cse1in its cytosolic state reveals a closed conformation incompatible with cargo binding. Mol Cell18:355–357Currie MG, Fok KF, Kato J, et al. (1992) Guanylin: an endogenous activator of intestinal guanylatecyclise. Proc Natl Acad Sci USA 89:947–951de Groot BL, Grubmüller H (2001) Water permeation across biological membranes: Mechanismand dynamics of aquaporin-1 and GlpF. Science 294:2353–2357de Groot BL, Amadei A, Scheek RM, et al. (1996a) An extended sampling of the configurationalspace of HPr from E coli. Proteins 26:314–322de Groot BL, Amadei A, van Aalten DMF, et al. (1996b) Towards an exhaustive sampling of theconfigurational spaces of the two forms of the peptide hormone guanylin. J Biomol Str Dyn13:741–751de Groot BL, van Aalten DMF, Scheek RM, et al. (1997) Prediction of protein conformationalfreedom from distance constraints. Proteins 29:240–251de Groot BL, Hayward S, van Aalten DMF, et al. (1998) Domain motions in bacteriophage T4lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins31:116–127de Groot BL, Vriend G, Berendsen HJC (1999) Conformational changes in the chaperoninGroEL: new insights into the allosteric mechanism. J Mol Biol 286:1241–1249de Groot BL, Engel A, Grubmüller H (2001) A refined structure of human Aquaporin-1. FEBSLett 504: 206–211de Groot BL, Frigato T, Helms V, et al. (2003) The mechanism of proton exclusion in theaquaporin-1 water channel. J Mol Biol 333:279–293Dixon MM, Nicholson H, Shewchuk L, et al. (1992) Structure of a hinge-bending bacteriophageT4 lysozyme mutant Ile3 → Pro. J Mol Biol 227:917–933
246 M.B. Kubitzki et al.Duda RO, Hart PE, Stork DG (2001) Pattern Classification, second edition. Wiley, New YorkFaber HR, Matthews BW (1990) A mutant T4 lysozyme displays five different crystal conformations.Nature 348:263–266Frauenfelder H, Leeson DT (1998) The energy landscape in non-biological and biological molecules.Nat Struct Biol 5:757–759Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins.Science 254:1598–1603Fu D, Libson A, Miercke LJ, et al. (2000) Structure of a glycerol-conducting channel and the basisfor its selectivity. Science 290: 481–486Fukunishi H, Watanabe O, Takada S (2002) On the Hamiltonian replica exchange method forefficient sampling of biomolecular systems: application to protein structure prediction. J ChemPhys 116:9058–9067García AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett68:2696–2699García AE, Onuchic JN (2003) Folding a protein in a computer: An atomic description of thefolding/unfolding of protein A. Proc Natl Acad Sci USA 100:13898–13903G N, Noguti T, Nishikawa T (1983) Dynamics of a small globular protein in terms of low-frequencyvibrational modes. Proc Natl Acad Sci USA 80:3696–3700Gerstein M, Lesk AM, Chothia C (1994) Structural mechanisms for domain movements in proteins.Biochemistry 33:6739–6749Gosh A, Rapp CS, Friesner RA (1998) Generalized Born model based on a surface integral formulation.J Phys Chem B 102:10983–10990Grubmüller H (1995) Predicting slow structural transitions in macromolecular systems:Conformational flooding. Phys Rev E 52:2893–2906Hansmann UHE (1997) Effective way for determination of multicanonical weights. Phys Rev E56:6200–6203Hayward S, Kitao A, Gō N (1995) Harmonicity and anharmonicity in protein dynamics: a normalmode analysis and principal component analysis. Proteins 23:177–186He J, Zhang Z, Shi Y, et al. (2003) Efficiently explore the energy landscape of proteins in moleculardynamics simulations by amplifying collective motions. J Chem Phys 119:4005–4017Hockney RW, Goel SP, Eastwood JW (1973) 10000 particle molecular dynamics model with longrangeforces. Chem Phys Lett 21:589–591Hub JS, de Groot BL (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. ProcNatl Acad Sci USA 105: 1198–1203Iba Y (2001) Extended ensemble Monte Carlo. Int J Mod Phys C 12:623–656Ilan B, Tajkhorshid E, Schulten K, et al. (2004) The mechanism of proton exclusion in aquaporinchannels. Proteins 55:223–228Jean-Charles A, Nicholls A, Sharp K, et al. (1991) Electrostatic contributions to solvation energies:comparison of free energy perturbation and continuum calculations. J Am Chem Soc113:1454–1455Jorgensen WL, Chandrasekhar J, Madura JD, et al. (1983) Comparison of simple potential functionsfor simulating liquid water. J Chem Phys 79:926–935Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS allatomforce field on conformational energetics and properties of organic liquids. J Am ChemSoc 118:11225–11236Karplus M, Gao YQ (2004) Biomolecular motors: the F1-ATPase paradigm. Curr Opin Struct Biol14:250–259Karplus M, Kushick JN (1981) Method for estimating the configurational entropy of macromolecules.Macromolecules 14:325–332Kempf JG, Loria JP (2003) Protein dynamics from solution NMR theory and applications. CellBiochem Biophys 37:187–211Kitao A, Gō N (1999) Investigating protein dynamics in collective coordinate space. Curr OpinStruct Biol 9:143–281
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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.
Page 202 and 203: 8 3D Motifs 195Table 8.1 (continued
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Page 210 and 211: 8 3D Motifs 203In addition to SITE
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Page 222 and 223: 8 3D Motifs 215Ivanisenko VA, Pintu
Page 224 and 225: Chapter 9Protein Dynamics: From Str
Page 226 and 227: 9 Protein Dynamics: From Structure
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
Page 264 and 265: 258 R.A. Laskowski10.2.5 Protein In
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
Page 272 and 273: 266 R.A. LaskowskiGly97Gly99Tyr98Ty
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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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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