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Volumn 43, Issue 3, 2009, Pages 131-143

Automated protein structure calculation from NMR data

Author keywords

Automation; Expert; NMR structure calculation of proteins; Programs; Structural genomics

Indexed keywords

ARTICLE; AUTOMATION; COMPUTER PROGRAM; FOURIER TRANSFORMATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; STRUCTURAL GENOMICS; STRUCTURE ANALYSIS;

EID: 61549100580     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-008-9295-6     Document Type: Article
Times cited : (53)

References (82)
  • 3
    • 4744344737 scopus 로고    scopus 로고
    • Automation of NMR structure determination of proteins
    • Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struct Biol 14:547-553
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 547-553
    • Altieri, A.S.1    Byrd, R.A.2
  • 4
    • 35448929112 scopus 로고    scopus 로고
    • A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing
    • Andrec M, Snyder DA, Zhou ZY, Young J, Montelione GT, Levy RM (2007) A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing. Proteins: Struct Funct Bioinf 69:449-465
    • (2007) Proteins: Struct Funct Bioinf , vol.69 , pp. 449-465
    • Andrec, M.1    Snyder, D.A.2    Zhou, Z.Y.3    Young, J.4    Montelione, G.T.5    Levy, R.M.6
  • 5
    • 3042788977 scopus 로고    scopus 로고
    • G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment
    • Atreya HS, Szyperski T (2004) G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment. Proc Natl Acad Sci USA 101:9642-9647
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9642-9647
    • Atreya, H.S.1    Szyperski, T.2
  • 6
    • 4344648451 scopus 로고    scopus 로고
    • Automated analysis of protein NMR assignments and structures
    • Baran MC, Huang YJ, Moseley HNB, Montelione GT (2004) Automated analysis of protein NMR assignments and structures. Chem Rev 104:3541-3555
    • (2004) Chem Rev , vol.104 , pp. 3541-3555
    • Baran, M.C.1    Huang, Y.J.2    Moseley, H.N.B.3    Montelione, G.T.4
  • 7
    • 0003007299 scopus 로고
    • Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments
    • Barna JCJ, Laue ED, Mayger MR, Skilling J, Worrall SJP (1987) Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments. J Magn Reson 73:69-77
    • (1987) J Magn Reson , vol.73 , pp. 69-77
    • Barna, J.C.J.1    Laue, E.D.2    Mayger, M.R.3    Skilling, J.4    Worrall, S.J.P.5
  • 8
    • 0343459675 scopus 로고
    • The program XEASY for computer-supported NMR spectral analysis of biological macromolecules
    • Bartels C, Xia TH, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1-10
    • (1995) J Biomol NMR , vol.6 , pp. 1-10
    • Bartels, C.1    Xia, T.H.2    Billeter, M.3    Güntert, P.4    Wüthrich, K.5
  • 9
    • 0000441606 scopus 로고    scopus 로고
    • GARANT - A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra
    • Bartels C, Güntert P, Billeter M, Wüthrich K (1997) GARANT - A general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comp Chem 18:139-149
    • (1997) J Comp Chem , vol.18 , pp. 139-149
    • Bartels, C.1    Güntert, P.2    Billeter, M.3    Wüthrich, K.4
  • 11
    • 55649119346 scopus 로고    scopus 로고
    • Solution NMR determination of proteins revisited
    • Billeter M, Wagner G, Wüthrich K (2008) Solution NMR determination of proteins revisited. J Biomol NMR 42:155-158
    • (2008) J Biomol NMR , vol.42 , pp. 155-158
    • Billeter, M.1    Wagner, G.2    Wüthrich, K.3
  • 13
    • 0033757822 scopus 로고    scopus 로고
    • An overview of structural genomics
    • Burley SK (2000) An overview of structural genomics. Nature Struct Biol 7:932-934
    • (2000) Nature Struct Biol , vol.7 , pp. 932-934
    • Burley, S.K.1
  • 14
    • 31144467558 scopus 로고    scopus 로고
    • The impact of structural genomics: Expectations and outcomes
    • Chandonia JM, Brenner SE (2006) The impact of structural genomics: expectations and outcomes. Science 311:347-351
    • (2006) Science , vol.311 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 15
    • 8844222708 scopus 로고    scopus 로고
    • TargetDB: A target registration database for structural genomics projects
    • Chen L, Oughtred R, Berman HM, Westbrook J (2004) TargetDB: A target registration database for structural genomics projects. Bioinformatics 20:2860-2862
    • (2004) Bioinformatics , vol.20 , pp. 2860-2862
    • Chen, L.1    Oughtred, R.2    Berman, H.M.3    Westbrook, J.4
  • 17
    • 33749159694 scopus 로고    scopus 로고
    • 'Big science' protein project under fire
    • Cyranoski D (2006) 'Big science' protein project under fire. Nature 443:382
    • (2006) Nature , vol.443 , pp. 382
    • Cyranoski, D.1
  • 20
    • 19944364336 scopus 로고    scopus 로고
    • Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data
    • Fossi M, Linge J, Labudde D, Leitner D, Nilges M, Oschkinat H (2005a) Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data. J Biomol NMR 31:21-34
    • (2005) J Biomol NMR , vol.31 , pp. 21-34
    • Fossi, M.1    Linge, J.2    Labudde, D.3    Leitner, D.4    Nilges, M.5    Oschkinat, H.6
  • 21
    • 19944407188 scopus 로고    scopus 로고
    • Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data
    • Fossi M, Oschkinat H, Nilges M, Ball LJ (2005b) Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data. J Magn Reson 175:92-102
    • (2005) J Magn Reson , vol.175 , pp. 92-102
    • Fossi, M.1    Oschkinat, H.2    Nilges, M.3    Ball, L.J.4
  • 23
    • 0037076277 scopus 로고    scopus 로고
    • CLOUDS, a protocol for deriving a molecular proton density via NMR
    • Grishaev A, Llinás M (2002) CLOUDS, a protocol for deriving a molecular proton density via NMR. Proc Natl Acad Sci USA 99:6707-6712
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 6707-6712
    • Grishaev, A.1    Llinás, M.2
  • 25
    • 1842486886 scopus 로고    scopus 로고
    • Automated structure determination of proteins by NMR spectroscopy
    • Gronwald W, Kalbitzer HR (2004) Automated structure determination of proteins by NMR spectroscopy. Progr Nucl Magn Reson Spectrosc 44:33-96
    • (2004) Progr Nucl Magn Reson Spectrosc , vol.44 , pp. 33-96
    • Gronwald, W.1    Kalbitzer, H.R.2
  • 26
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Güntert P, Mumenthaler C, Wüthrich K (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273:283-298
    • (1997) J Mol Biol , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 27
    • 4344698912 scopus 로고    scopus 로고
    • Automated NMR protein structure calculation
    • Güntert P (2003) Automated NMR protein structure calculation. Progr NMR Spectrosc 43:105-125
    • (2003) Progr NMR Spectrosc , vol.43 , pp. 105-125
    • Güntert, P.1
  • 28
    • 58849162221 scopus 로고    scopus 로고
    • Automated structure determination from NMR spectra
    • (in press)
    • Güntert P (2008) Automated structure determination from NMR spectra. Eur Biophys J 38 (in press)
    • (2008) Eur Biophys J , vol.38
    • Güntert, P.1
  • 29
    • 0033757915 scopus 로고    scopus 로고
    • Structural genomics in Europe: Slow start, strong finish?
    • Heinemann U (2000) Structural genomics in Europe: Slow start, strong finish? Nature Struct Biol 7:940-942
    • (2000) Nature Struct Biol , vol.7 , pp. 940-942
    • Heinemann, U.1
  • 30
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209-227
    • (2002) J Mol Biol , vol.319 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wüthrich, K.3
  • 31
    • 34848903007 scopus 로고    scopus 로고
    • Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR Spectroscopy
    • Hiller S, Wasmer C, Wider G, Wüthrich K (2007) Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR Spectroscopy. J Am Chem Soc 129:10823-10828
    • (2007) J Am Chem Soc , vol.129 , pp. 10823-10828
    • Hiller, S.1    Wasmer, C.2    Wider, G.3    Wüthrich, K.4
  • 32
    • 0037266406 scopus 로고    scopus 로고
    • MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins
    • Hitchens TK, Lukin JA, Zhan YP, McCallum SA, Rule GS (2003) MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. J Biomol NMR 25:1-9
    • (2003) J Biomol NMR , vol.25 , pp. 1-9
    • Hitchens, T.K.1    Lukin, J.A.2    Zhan, Y.P.3    McCallum, S.A.4    Rule, G.S.5
  • 34
    • 34548484836 scopus 로고    scopus 로고
    • Perspectives of biomolecular NMR in drug discovery: The blessing and curse of versatility
    • Jahnke W (2007) Perspectives of biomolecular NMR in drug discovery: The blessing and curse of versatility. J Biomol NMR 39:87-90
    • (2007) J Biomol NMR , vol.39 , pp. 87-90
    • Jahnke, W.1
  • 35
    • 0242355012 scopus 로고    scopus 로고
    • Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment
    • Jee J, Güntert P (2003) Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment. J Struct Funct Genomics 4:179-189
    • (2003) J Struct Funct Genomics , vol.4 , pp. 179-189
    • Jee, J.1    Güntert, P.2
  • 36
    • 34249765651 scopus 로고
    • NMRView: A computer program for the visualization and analysis of NMR data
    • Johnson BA, Blevins RA (1994) NMRView: A computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
    • (1994) J Biomol NMR , vol.4 , pp. 603-614
    • Johnson, B.A.1    Blevins, R.A.2
  • 37
    • 32144464187 scopus 로고    scopus 로고
    • An efficient randomized algorithm for contact-based NMR backbone resonance assignment
    • Kamisetty H, Bailey-Kellogg C, Pandurangan G (2006) An efficient randomized algorithm for contact-based NMR backbone resonance assignment. Bioinformatics 22:172-180
    • (2006) Bioinformatics , vol.22 , pp. 172-180
    • Kamisetty, H.1    Bailey-Kellogg, C.2    Pandurangan, G.3
  • 38
    • 34547923673 scopus 로고    scopus 로고
    • KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
    • Kobayashi N, Iwahara J, Koshiba S, Tomizawa T, Tochio N, Güntert P, Kigawa T, Yokoyama S (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR 39:31-52
    • (2007) J Biomol NMR , vol.39 , pp. 31-52
    • Kobayashi, N.1    Iwahara, J.2    Koshiba, S.3    Tomizawa, T.4    Tochio, N.5    Güntert, P.6    Kigawa, T.7    Yokoyama, S.8
  • 40
    • 2442687868 scopus 로고    scopus 로고
    • Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy
    • Kupěe E, Freeman R (2004) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126:6429-6440
    • (2004) J Am Chem Soc , vol.126 , pp. 6429-6440
    • Kupěe, E.1    Freeman, R.2
  • 41
    • 2442717620 scopus 로고    scopus 로고
    • Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments
    • Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, Clore GM (2004) Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126:6258-6273
    • (2004) J Am Chem Soc , vol.126 , pp. 6258-6273
    • Kuszewski, J.1    Schwieters, C.D.2    Garrett, D.S.3    Byrd, R.A.4    Tjandra, N.5    Clore, G.M.6
  • 42
    • 50449105226 scopus 로고    scopus 로고
    • Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: Improved robustness and performance of the PASD algorithm
    • Kuszewski JJ, Thottungal RA, Clore GM, Schwieters CD (2008) Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: Improved robustness and performance of the PASD algorithm. J Biomol NMR 41:221-239
    • (2008) J Biomol NMR , vol.41 , pp. 221-239
    • Kuszewski, J.J.1    Thottungal, R.A.2    Clore, G.M.3    Schwieters, C.D.4
  • 43
    • 33847616971 scopus 로고    scopus 로고
    • Growth of novel protein structural data
    • Levitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104:3183-3188
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 3183-3188
    • Levitt, M.1
  • 44
    • 0037316363 scopus 로고    scopus 로고
    • ARIA: Automated NOE assignment and NMR structure calculation
    • Linge JP, Habeck M, Rieping W, Nilges M (2003a) ARIA: Automated NOE assignment and NMR structure calculation. Bioinformatics 19:315-316
    • (2003) Bioinformatics , vol.19 , pp. 315-316
    • Linge, J.P.1    Habeck, M.2    Rieping, W.3    Nilges, M.4
  • 47
    • 33749524593 scopus 로고    scopus 로고
    • Automated protein structure determination from NMR spectra
    • López-Méndez B, Güntert P (2006) Automated protein structure determination from NMR spectra. J Am Chem Soc 128:13112-13122
    • (2006) J Am Chem Soc , vol.128 , pp. 13112-13122
    • López-Méndez, B.1    Güntert, P.2
  • 48
    • 0043027070 scopus 로고    scopus 로고
    • Fully automated sequence-specific resonance assignments of heteronuclear protein spectra
    • Malmodin D, Papavoine CHM, Billeter M (2003) Fully automated sequence-specific resonance assignments of heteronuclear protein spectra. J Biomol NMR 27:69-79
    • (2003) J Biomol NMR , vol.27 , pp. 69-79
    • Malmodin, D.1    Papavoine, C.H.M.2    Billeter, M.3
  • 49
    • 19944411144 scopus 로고    scopus 로고
    • High-throughput analysis of protein NMR spectra
    • Malmodin D, Billeter M (2005) High-throughput analysis of protein NMR spectra. Progr NMR Spectrosc 46:109-129
    • (2005) Progr NMR Spectrosc , vol.46 , pp. 109-129
    • Malmodin, D.1    Billeter, M.2
  • 50
    • 52949121796 scopus 로고    scopus 로고
    • Structural biology by NMR: Structure, dynamics and interactions
    • Markwick PRL, Malliavin T, Nilges M (2008) Structural biology by NMR: structure, dynamics and interactions. PLOS Comput Biol 4:e1000168
    • (2008) PLOS Comput Biol , vol.4
    • Markwick, P.R.L.1    Malliavin, T.2    Nilges, M.3
  • 51
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • Meiler J, Baker D (2003) Rapid protein fold determination using unassigned NMR data. Proc Natl Acad Sci USA 100:15404-15409
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 52
    • 0034923123 scopus 로고    scopus 로고
    • Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data
    • Moseley HNB, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91-108
    • (2001) Methods Enzymol , vol.339 , pp. 91-108
    • Moseley, H.N.B.1    Monleon, D.2    Montelione, G.T.3
  • 53
    • 4544269370 scopus 로고    scopus 로고
    • A generalized approach to automated NMR peak list editing: Application to reduced dimensionality triple resonance spectra
    • Moseley HNB, Riaz N, Aramini JM, Szyperski T, Montelione GT (2004a) A generalized approach to automated NMR peak list editing: Application to reduced dimensionality triple resonance spectra. J Magn Reson 170:263-277
    • (2004) J Magn Reson , vol.170 , pp. 263-277
    • Moseley, H.N.B.1    Riaz, N.2    Aramini, J.M.3    Szyperski, T.4    Montelione, G.T.5
  • 54
    • 1442306656 scopus 로고    scopus 로고
    • Assignment validation software suite for the evaluation and presentation of protein resonance assignment data
    • Moseley HNB, Sahota G, Montelione GT (2004b) Assignment validation software suite for the evaluation and presentation of protein resonance assignment data. J Biomol NMR 28:341-355
    • (2004) J Biomol NMR , vol.28 , pp. 341-355
    • Moseley, H.N.B.1    Sahota, G.2    Montelione, G.T.3
  • 57
    • 0028907436 scopus 로고
    • Calculation of protein structures with ambiguous distance restraints: Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities
    • Nilges M (1995) Calculation of protein structures with ambiguous distance restraints: Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities. J Mol Biol 245:645-660
    • (1995) J Mol Biol , vol.245 , pp. 645-660
    • Nilges, M.1
  • 58
    • 0347988396 scopus 로고    scopus 로고
    • Ambiguous NOEs and automated NOE assignment
    • Nilges M, O'Donoghue SI (1998) Ambiguous NOEs and automated NOE assignment. Progr NMR Spectrosc 32:107-139
    • (1998) Progr NMR Spectrosc , vol.32 , pp. 107-139
    • Nilges, M.1    O'Donoghue, S.I.2
  • 59
    • 15844424159 scopus 로고    scopus 로고
    • APART: Automated preprocessing for NMR assignments with reduced tedium
    • Pawley NH, Gans JD, Michalczyk R (2005) APART: Automated preprocessing for NMR assignments with reduced tedium. Bioinformatics 21:680-682
    • (2005) Bioinformatics , vol.21 , pp. 680-682
    • Pawley, N.H.1    Gans, J.D.2    Michalczyk, R.3
  • 63
    • 33746238240 scopus 로고    scopus 로고
    • Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra
    • Scott A, López-Méndez B, Güntert P (2006) Fully automated structure determinations of the Fes SH2 domain using different sets of NMR spectra. Magn Reson Chem 44:S83-S88
    • (2006) Magn Reson Chem , vol.44
    • Scott, A.1    López-Méndez, B.2    Güntert, P.3
  • 64
    • 21244479278 scopus 로고    scopus 로고
    • G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination
    • Shen Y, Atreya HS, Liu GH, Szyperski T (2005) G-matrix Fourier transform NOESY-based protocol for high-quality protein structure determination. J Am Chem Soc 127:9085-9099
    • (2005) J Am Chem Soc , vol.127 , pp. 9085-9099
    • Shen, Y.1    Atreya, H.S.2    Liu, G.H.3    Szyperski, T.4
  • 66
    • 36349027062 scopus 로고    scopus 로고
    • Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: Application to the RRMs of Npl3p and hnRNP L
    • Skrisovska L, Allain FHT (2008) Improved segmental isotope labeling methods for the NMR study of multidomain or large proteins: Application to the RRMs of Npl3p and hnRNP L. J Mol Biol 375:151-164
    • (2008) J Mol Biol , vol.375 , pp. 151-164
    • Skrisovska, L.1    Allain, F.H.T.2
  • 67
    • 0142211244 scopus 로고    scopus 로고
    • Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments
    • Slupsky CM, Boyko RF, Booth VK, Sykes BD (2003) Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments. J Biomol NMR 27:313-321
    • (2003) J Biomol NMR , vol.27 , pp. 313-321
    • Slupsky, C.M.1    Boyko, R.F.2    Booth, V.K.3    Sykes, B.D.4
  • 71
    • 39149093421 scopus 로고    scopus 로고
    • Automated structure determination of proteins with the SAIL-FLYA NMR method
    • Takeda M, Ikeya T, Güntert P, Kainosho M (2007) Automated structure determination of proteins with the SAIL-FLYA NMR method. Nat Protoc 2:2896-2902
    • (2007) Nat Protoc , vol.2 , pp. 2896-2902
    • Takeda, M.1    Ikeya, T.2    Güntert, P.3    Kainosho, M.4
  • 72
    • 0033757870 scopus 로고    scopus 로고
    • Structural genomics in North America
    • Terwilliger TC (2000) Structural genomics in North America. Nature Struct Biol 7:935-939
    • (2000) Nature Struct Biol , vol.7 , pp. 935-939
    • Terwilliger, T.C.1


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