메뉴 건너뛰기




Volumn 4, Issue 1, 2009, Pages

Similarity measures for protein ensembles

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 58449108594     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004203     Document Type: Article
Times cited : (66)

References (84)
  • 1
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nature Struct Biol 9: 646-652.
    • (2002) Nature Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 3
    • 0025943869 scopus 로고
    • Exploration of disorder in protein structures by X-ray restrained molecular dynamics
    • Kuriyan J, et al. (1991) Exploration of disorder in protein structures by X-ray restrained molecular dynamics. Proteins 10: 340-358.
    • (1991) Proteins , vol.10 , pp. 340-358
    • Kuriyan, J.1
  • 4
    • 2342525085 scopus 로고    scopus 로고
    • Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography
    • DePristo MA, de Bakker PI, Blundell TL (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure 12: 831-838.
    • (2004) Structure , vol.12 , pp. 831-838
    • DePristo, M.A.1    de Bakker, P.I.2    Blundell, T.L.3
  • 7
    • 33846532929 scopus 로고    scopus 로고
    • The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins
    • Richter B, Gsponer J, Varnai P, Salvatella X, Vendruscolo M (2007) The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR 37: 117-135.
    • (2007) J Biomol NMR , vol.37 , pp. 117-135
    • Richter, B.1    Gsponer, J.2    Varnai, P.3    Salvatella, X.4    Vendruscolo, M.5
  • 8
    • 34548387498 scopus 로고    scopus 로고
    • Ensemble refinement of protein crystal structures: Validation and application
    • Levin EJ, Kondrashov DA, Wesenberg GE, Phillips Jr GN (2007) Ensemble refinement of protein crystal structures: Validation and application. Structure 15: 1040-1052.
    • (2007) Structure , vol.15 , pp. 1040-1052
    • Levin, E.J.1    Kondrashov, D.A.2    Wesenberg, G.E.3    Phillips Jr, G.N.4
  • 9
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W, Habeck H, Nilges M (2005) Inferential structure determination. Science 309: 303-306.
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, H.2    Nilges, M.3
  • 11
    • 0041510360 scopus 로고    scopus 로고
    • Structural genomics: Computational methods for structure analysis
    • Goldsmith-Fischman S, Honig B (2003) Structural genomics: Computational methods for structure analysis. Prot Sci 12: 1813-1821.
    • (2003) Prot Sci , vol.12 , pp. 1813-1821
    • Goldsmith-Fischman, S.1    Honig, B.2
  • 12
    • 1342289274 scopus 로고    scopus 로고
    • Sensitivity and selectivity in protein structure comparison
    • Sierk ML, Pearson WR (2004) Sensitivity and selectivity in protein structure comparison. Prot Sci 13: 773-785.
    • (2004) Prot Sci , vol.13 , pp. 773-785
    • Sierk, M.L.1    Pearson, W.R.2
  • 13
    • 0037230925 scopus 로고    scopus 로고
    • Efficient RMSD measures for the comparison of two molecular ensembles
    • Brüschweiler R (2003) Efficient RMSD measures for the comparison of two molecular ensembles. Proteins 50: 26-34.
    • (2003) Proteins , vol.50 , pp. 26-34
    • Brüschweiler, R.1
  • 14
    • 33846512402 scopus 로고    scopus 로고
    • A consensus view of protein dynamics
    • Rueda M, et al. (2007) A consensus view of protein dynamics. Proc Natl Acad Sci USA 104: 796-801.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 796-801
    • Rueda, M.1
  • 15
    • 0034500645 scopus 로고    scopus 로고
    • Similarities between principal components of protein dynamics and random diffusion
    • Hess B (2000) Similarities between principal components of protein dynamics and random diffusion. Phys Rev E 62: 8438-8448.
    • (2000) Phys Rev E , vol.62 , pp. 8438-8448
    • Hess, B.1
  • 16
    • 41349089279 scopus 로고    scopus 로고
    • Convergence of sampling in protein simulations
    • Hess B (2002) Convergence of sampling in protein simulations. Phys Rev E 65: 031910.
    • (2002) Phys Rev E , vol.65 , pp. 031910
    • Hess, B.1
  • 17
    • 0029022355 scopus 로고
    • Conformational variability of solution nuclear magnetic resonance structures
    • Bonvin AMJJ, Brünger AT (1995) Conformational variability of solution nuclear magnetic resonance structures. J Mol Biol 250: 80-93.
    • (1995) J Mol Biol , vol.250 , pp. 80-93
    • Bonvin, A.M.J.J.1    Brünger, A.T.2
  • 18
    • 0029693351 scopus 로고    scopus 로고
    • Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?
    • Bonvin AMJJ, Brünger AT (1996) Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? J Biomol NMR 7: 72-76.
    • (1996) J Biomol NMR , vol.7 , pp. 72-76
    • Bonvin, A.M.J.J.1    Brünger, A.T.2
  • 19
    • 33745759471 scopus 로고    scopus 로고
    • Ensemble-based convergence analysis of biomolecular trajectories
    • Lyman E, Zuckerman DM (2006) Ensemble-based convergence analysis of biomolecular trajectories. Biophys J 91: 164-172.
    • (2006) Biophys J , vol.91 , pp. 164-172
    • Lyman, E.1    Zuckerman, D.M.2
  • 20
    • 0041845254 scopus 로고    scopus 로고
    • Non-parametric estimation of distance between groups
    • Krzanowski WJ (2003) Non-parametric estimation of distance between groups. J Appl Stat 30: 743-750.
    • (2003) J Appl Stat , vol.30 , pp. 743-750
    • Krzanowski, W.J.1
  • 21
    • 33645988196 scopus 로고    scopus 로고
    • From sample similarity to ensemble similarity: Probabilistic distance measures in reproducing kernel Hilbert space
    • Zhou S, Chellappa R (2006) From sample similarity to ensemble similarity: Probabilistic distance measures in reproducing kernel Hilbert space. IEEE Trans Pattern Anal Mach Intell 28: 917-929.
    • (2006) IEEE Trans Pattern Anal Mach Intell , vol.28 , pp. 917-929
    • Zhou, S.1    Chellappa, R.2
  • 24
    • 0035305311 scopus 로고    scopus 로고
    • Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations
    • Qian H (2001) Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations. Phys Rev E 63: 042103.
    • (2001) Phys Rev E , vol.63 , pp. 042103
    • Qian, H.1
  • 25
    • 58449121512 scopus 로고    scopus 로고
    • Clemente-Gallardo J, Moreno Y, Lorenzo JFS, Velazquez-Campoy A, eds. New York, USA: American Institute of Physics. pp
    • Wall ME (2006) Ligand binding, protein fluctuations, and allosteric free energy. Clemente-Gallardo J, Moreno Y, Lorenzo JFS, Velazquez-Campoy A, eds. New York, USA: American Institute of Physics. pp 16-33.
    • (2006) Ligand binding, protein fluctuations, and allosteric free energy , pp. 16-33
    • Wall, M.E.1
  • 26
    • 84873751778 scopus 로고
    • An invariant form for the prior probability in estimation problems
    • Jeffreys H (1946) An invariant form for the prior probability in estimation problems. Proc R Soc Lond A 186: 453-461.
    • (1946) Proc R Soc Lond A , vol.186 , pp. 453-461
    • Jeffreys, H.1
  • 28
    • 0025952277 scopus 로고
    • Divergence measures based on the Shannon entropy
    • Lin J (1991) Divergence measures based on the Shannon entropy. IEEE Trans Inf Theory 37: 145-151.
    • (1991) IEEE Trans Inf Theory , vol.37 , pp. 145-151
    • Lin, J.1
  • 29
    • 10744227947 scopus 로고    scopus 로고
    • A new class of metric divergences on probability spaces and its applicability in statistics
    • Össterreicher F, Vajda I (2003) A new class of metric divergences on probability spaces and its applicability in statistics. Ann Inst Statist Math 55: 639-653.
    • (2003) Ann Inst Statist Math , vol.55 , pp. 639-653
    • Össterreicher, F.1    Vajda, I.2
  • 32
    • 84964203940 scopus 로고
    • Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy
    • Efron B, Tibshirani R (1986) Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat Sci 1: 54-75.
    • (1986) Stat Sci , vol.1 , pp. 54-75
    • Efron, B.1    Tibshirani, R.2
  • 33
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • Frey BJ, Dueck D (2007) Clustering by passing messages between data points. Science 315: 972-976.
    • (2007) Science , vol.315 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 34
    • 0037059052 scopus 로고    scopus 로고
    • A self-organizing principle for learning nonlinear manifolds
    • Agrafiotis DK, Xu H (2002) A self-organizing principle for learning nonlinear manifolds. Proc Natl Acad Sci USA 99: 15869-15872.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 15869-15872
    • Agrafiotis, D.K.1    Xu, H.2
  • 36
    • 0001473437 scopus 로고
    • On estimation of probability density function and mode
    • Parzen E (1962) On estimation of probability density function and mode. Ann Math Statist 33: 1065-1076.
    • (1962) Ann Math Statist , vol.33 , pp. 1065-1076
    • Parzen, E.1
  • 39
    • 0041171994 scopus 로고
    • On optimal data-based bandwidth selection in kernel density estimation
    • Hall P, Sheather SJ, Jones MC, Marron JS (1991) On optimal data-based bandwidth selection in kernel density estimation. Biometrika 78: 263-269.
    • (1991) Biometrika , vol.78 , pp. 263-269
    • Hall, P.1    Sheather, S.J.2    Jones, M.C.3    Marron, J.S.4
  • 40
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular dynamics system
    • Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular dynamics system. J Chem Phys 105: 1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 41
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for protein dynamics and thermodynamics
    • Lazaridis T, Karplus M (1999) Effective energy function for protein dynamics and thermodynamics. Proteins 35: 133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 42
    • 0041784950 scopus 로고    scopus 로고
    • All-atom empirical potential for molecular modeling and dynamics studies of proteins
    • MacKerell Jr AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102: 3586-3616.
    • (1998) J Phys Chem B , vol.102 , pp. 3586-3616
    • MacKerell Jr, A.D.1
  • 43
    • 1642576012 scopus 로고    scopus 로고
    • Improved treatment of the protein backbone in empirical force fields
    • MacKerell Jr AD, Feig M, Brooks III CL (2004) Improved treatment of the protein backbone in empirical force fields. J Am Chem Soc 126: 698-699.
    • (2004) J Am Chem Soc , vol.126 , pp. 698-699
    • MacKerell Jr, A.D.1    Feig, M.2    Brooks III, C.L.3
  • 44
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im W, Lee MS, Brooks III CL (2003) Generalized born model with a simple smoothing function. J Comp Chem 24: 1691-1702.
    • (2003) J Comp Chem , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks III, C.L.3
  • 45
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 23: 327-341.
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 46
    • 36749110658 scopus 로고
    • Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances
    • Tropp J (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J Chem Phys 72: 6035-6043.
    • (1980) J Chem Phys , vol.72 , pp. 6035-6043
    • Tropp, J.1
  • 48
    • 0001767250 scopus 로고
    • Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution
    • Brüschweiler R, et al. (1992) Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J Am Chem Soc 114: 2289-2302.
    • (1992) J Am Chem Soc , vol.114 , pp. 2289-2302
    • Brüschweiler, R.1
  • 49
    • 0344791680 scopus 로고    scopus 로고
    • Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory
    • Schneider T, Brünger AT, Nilges M (1999) Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory. J Mol Biol 285: 727-740.
    • (1999) J Mol Biol , vol.285 , pp. 727-740
    • Schneider, T.1    Brünger, A.T.2    Nilges, M.3
  • 50
    • 0026559517 scopus 로고
    • Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance
    • Post CB (1992) Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance. J Mol Biol 224: 1087-1101.
    • (1992) J Mol Biol , vol.224 , pp. 1087-1101
    • Post, C.B.1
  • 52
    • 0028854127 scopus 로고
    • Dominant solvation effects from the primary shell of hydration - approximation for molecular-dynamics simulations
    • Beglov D, Roux B (1995) Dominant solvation effects from the primary shell of hydration - approximation for molecular-dynamics simulations. Biopolymers 35: 171-178.
    • (1995) Biopolymers , vol.35 , pp. 171-178
    • Beglov, D.1    Roux, B.2
  • 53
    • 0033531973 scopus 로고    scopus 로고
    • Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
    • Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations. J Mol Biol 288: 441-459.
    • (1999) J Mol Biol , vol.288 , pp. 441-459
    • Paci, E.1    Karplus, M.2
  • 54
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization and dynamics calculations
    • Brooks BR, et al. (1983) CHARMM: A program for macromolecular energy, minimization and dynamics calculations. J Comp Chem 4: 187-217.
    • (1983) J Comp Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 55
    • 0000885331 scopus 로고
    • Harmonic analysis of large systems. I. Methodology
    • Brooks BR, Janežič D, Karplus M (1995) Harmonic analysis of large systems. I. Methodology. J Comp Chem 16: 1522-1542.
    • (1995) J Comp Chem , vol.16 , pp. 1522-1542
    • Brooks, B.R.1    Janežič, D.2    Karplus, M.3
  • 56
    • 44149084366 scopus 로고
    • An application of information theory to multivariate analysis
    • Kullback S (1952) An application of information theory to multivariate analysis. Ann Math Statist 23: 88-102.
    • (1952) Ann Math Statist , vol.23 , pp. 88-102
    • Kullback, S.1
  • 57
    • 0002975203 scopus 로고
    • On the generalised distance in statistics
    • Mahalanobis P (1936) On the generalised distance in statistics. Proc Natl Inst Sci India 12: 49-55.
    • (1936) Proc Natl Inst Sci India , vol.12 , pp. 49-55
    • Mahalanobis, P.1
  • 58
    • 0346961488 scopus 로고    scopus 로고
    • A well-conditioned estimator for large-dimensional covariance matrices
    • Ledoit O, Wolf M (2004) A well-conditioned estimator for large-dimensional covariance matrices. J Multivar Anal 88: 365-411.
    • (2004) J Multivar Anal , vol.88 , pp. 365-411
    • Ledoit, O.1    Wolf, M.2
  • 59
    • 58449091376 scopus 로고    scopus 로고
    • Statistical characterization of protein ensembles. IEEE/ACM Trans Comput Biol
    • In press
    • Rother D, Sapiro G, Pande V (2007) Statistical characterization of protein ensembles. IEEE/ACM Trans Comput Biol Bioinform, (In press).
    • (2007) Bioinform
    • Rother, D.1    Sapiro, G.2    Pande, V.3
  • 60
    • 0021104755 scopus 로고
    • Molecular dynamics of native protein. II. Analysis and nature of motion
    • Levitt M (1983) Molecular dynamics of native protein. II. Analysis and nature of motion. J Mol Biol 168: 621-657.
    • (1983) J Mol Biol , vol.168 , pp. 621-657
    • Levitt, M.1
  • 61
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao A, Go N (1999) Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 9: 164-169.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 64
    • 33847026420 scopus 로고    scopus 로고
    • Statistical validation of the root-mean-square-distance, a measure of protein structural proximity
    • Carugo O (2007) Statistical validation of the root-mean-square-distance, a measure of protein structural proximity. Prot Eng Des Sel 20: 33-37.
    • (2007) Prot Eng Des Sel , vol.20 , pp. 33-37
    • Carugo, O.1
  • 65
    • 0034704229 scopus 로고    scopus 로고
    • A global geometric framework for nonlinear dimensionality reduction
    • Tenenbaum JB, de Silva V, Langford JC (2000) A global geometric framework for nonlinear dimensionality reduction. Science 290: 2319-2323.
    • (2000) Science , vol.290 , pp. 2319-2323
    • Tenenbaum, J.B.1    de Silva, V.2    Langford, J.C.3
  • 67
    • 33745611125 scopus 로고    scopus 로고
    • Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
    • Das P, Moll M, Stamati H, Kavraki LE, Clementi C (2006) Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci USA 103: 9885-9890.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 9885-9890
    • Das, P.1    Moll, M.2    Stamati, H.3    Kavraki, L.E.4    Clementi, C.5
  • 68
    • 33645033314 scopus 로고    scopus 로고
    • Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?
    • Zagrovic B, van Gunsteren WF (2006) Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us? Proteins 63: 210-218.
    • (2006) Proteins , vol.63 , pp. 210-218
    • Zagrovic, B.1    van Gunsteren, W.F.2
  • 69
    • 18844409482 scopus 로고    scopus 로고
    • Quantifying allosteric effects in proteins
    • Ming D, Wall ME (2005) Quantifying allosteric effects in proteins. Proteins 59: 697-707.
    • (2005) Proteins , vol.59 , pp. 697-707
    • Ming, D.1    Wall, M.E.2
  • 71
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance-matrix
    • Schlitter J (1993) Estimation of absolute and relative entropies of macromolecules using the covariance-matrix. Chem Phys Lett 215: 617-621.
    • (1993) Chem Phys Lett , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 72
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M (2001) On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 115: 6289-6292.
    • (2001) J Chem Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 73
    • 33847361456 scopus 로고    scopus 로고
    • Convergence of molecular dynamics simulations of membrane proteins
    • Grossfield A, Feller SE, Pitman MC (2007) Convergence of molecular dynamics simulations of membrane proteins. Proteins 67: 31-40.
    • (2007) Proteins , vol.67 , pp. 31-40
    • Grossfield, A.1    Feller, S.E.2    Pitman, M.C.3
  • 75
    • 0033105674 scopus 로고    scopus 로고
    • Molecular dynamics and accuracy of NMR structures: Effects of error bounds and data removal
    • Chalaoux FR, O'Donoghue SI, Nilges M (1999) Molecular dynamics and accuracy of NMR structures: Effects of error bounds and data removal. Proteins 34: 453-463.
    • (1999) Proteins , vol.34 , pp. 453-463
    • Chalaoux, F.R.1    O'Donoghue, S.I.2    Nilges, M.3
  • 76
    • 84860040254 scopus 로고    scopus 로고
    • Simulation studies of the fidelity of biomolecular structure ensemble recreation
    • Latzer J, Eastwood MP, Wolynes PG (2006) Simulation studies of the fidelity of biomolecular structure ensemble recreation. J Chem Phys 125: 214905.
    • (2006) J Chem Phys , vol.125 , pp. 214905
    • Latzer, J.1    Eastwood, M.P.2    Wolynes, P.G.3
  • 77
    • 34547726188 scopus 로고    scopus 로고
    • Transition states for protein folding using molecular dynamics and experimental restraints
    • Allen LR, Paci E (2007) Transition states for protein folding using molecular dynamics and experimental restraints. J of Phys: Condensed Matter 19: 285211.
    • (2007) J of Phys: Condensed Matter , vol.19 , pp. 285211
    • Allen, L.R.1    Paci, E.2
  • 78
    • 0030038545 scopus 로고    scopus 로고
    • Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
    • Burling FT, Weis WI, Flaherty KM, Brünger AT (1996) Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271: 72-77.
    • (1996) Science , vol.271 , pp. 72-77
    • Burling, F.T.1    Weis, W.I.2    Flaherty, K.M.3    Brünger, A.T.4
  • 79
    • 29444446536 scopus 로고    scopus 로고
    • Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α/β protein: A unified picture of high probability, fast atomic motions in proteins
    • Clore GM, Schwieters CD (2006) Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small α/β protein: A unified picture of high probability, fast atomic motions in proteins. J Mol Biol 355: 879-886.
    • (2006) J Mol Biol , vol.355 , pp. 879-886
    • Clore, G.M.1    Schwieters, C.D.2
  • 80
    • 33846215187 scopus 로고    scopus 로고
    • Quality assurance for biomolecular simulations
    • Murdock SE, et al. (2006) Quality assurance for biomolecular simulations. J Chem Theory Comp 2: 1477-1481.
    • (2006) J Chem Theory Comp , vol.2 , pp. 1477-1481
    • Murdock, S.E.1
  • 81
    • 12144275299 scopus 로고    scopus 로고
    • Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
    • Beck DA, Armen RS, Daggett V (2005) Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 44: 609-616.
    • (2005) Biochemistry , vol.44 , pp. 609-616
    • Beck, D.A.1    Armen, R.S.2    Daggett, V.3
  • 82
    • 0032710610 scopus 로고    scopus 로고
    • Increased protein backbone conformational entropy upon hydrophobic ligand binding
    • Zídek L, Novotny MV, Stone MJ (1999) Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nature Struct Biol 6: 1118-1121.
    • (1999) Nature Struct Biol , vol.6 , pp. 1118-1121
    • Zídek, L.1    Novotny, M.V.2    Stone, M.J.3
  • 83
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr DD, McElheny D, Dyson HJ, Wright PE (2006) The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313: 1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 84
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D, Zuiderweg ER (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13: 748-757.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.