메뉴 건너뛰기




Volumn 50, Issue 2, 2011, Pages 147-155

RelaxGUI: A new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ls motion of proteins

Author keywords

Graphical user interface; GUI; Lipari and Szabo model free analysis; NMR spin relaxation; Protein dynamics; Relax software

Indexed keywords

ARTICLE; CHEMICAL STRUCTURE; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; RELAXGUI;

EID: 80955177559     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-011-9509-1     Document Type: Article
Times cited : (52)

References (26)
  • 1
    • 0000501656 scopus 로고
    • Information theory and an extension of the maximum likelihood principle
    • Petrov BN, Csaki F (eds), Akademia Kiado
    • Akaike H (1973) Information theory and an extension of the maximum likelihood principle. In: Petrov BN, Csaki F (eds) Proceedings of the second international symposium on information theory, Budapest, Akademia Kiado, pp 267-281
    • (1973) Proceedings of the Second International Symposium on Information Theory, Budapest , pp. 267-281
    • Akaike, H.1
  • 3
    • 0025046144 scopus 로고
    • Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
    • DOI 10.1021/ja00168a070
    • Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM (1990) Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins. J Am Chem Soc 112(12):4989-4991 (Pubitemid 20285925)
    • (1990) Journal of the American Chemical Society , vol.112 , Issue.12 , pp. 4989-4991
    • Clore, G.M.1    Szabo, A.2    Bax, A.3    Kay, L.E.4    Driscoll, P.C.5    Gronenborn, A.M.6
  • 4
    • 0038068865 scopus 로고    scopus 로고
    • FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data
    • DOI 10.1023/A:1023808801134
    • Cole R, Loria JP (2003) FAST-Modelfree: a program for rapid automated analysis of solution NMR spin-relaxation data. J Biomol NMR 26(3):203-213 (Pubitemid 36758441)
    • (2003) Journal of Biomolecular NMR , vol.26 , Issue.3 , pp. 203-213
    • Cole, R.1    Loria, J.P.2
  • 5
    • 0037266991 scopus 로고    scopus 로고
    • The use of model selection in the model-free analysis of protein dynamics
    • DOI 10.1023/A:1021902006114
    • d'Auvergne EJ, Gooley PR (2003) The use of model selection in the model-free analysis of protein dynamics. J Biomol NMR 25(1): 25-39 (Pubitemid 36181759)
    • (2003) Journal of Biomolecular NMR , vol.25 , Issue.1 , pp. 25-39
    • D'Auvergne, E.J.1    Gooley, P.R.2
  • 6
    • 33745623124 scopus 로고    scopus 로고
    • Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data
    • DOI 10.1007/s10858-006-9007-z
    • d'Auvergne EJ, Gooley PR (2006) Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data. J Biomol NMR 35(2):117-135. doi:10.1007/s10858-006-9007-z (Pubitemid 43986214)
    • (2006) Journal of Biomolecular NMR , vol.35 , Issue.2 , pp. 117-135
    • D'Auvergne, E.J.1    Gooley, P.R.2
  • 7
    • 34250781656 scopus 로고    scopus 로고
    • Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm
    • DOI 10.1039/b702202f
    • d'Auvergne EJ, Gooley PR (2007) Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol Biosyst 3(7):483-494. doi:10.1039/b702202f (Pubitemid 46961676)
    • (2007) Molecular BioSystems , vol.3 , Issue.7 , pp. 483-494
    • D'auvergne, E.J.1    Gooley, P.R.2
  • 8
    • 38349077155 scopus 로고    scopus 로고
    • Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces
    • doi:10.1007/s10858-007-9214-2
    • d'Auvergne EJ, Gooley PR (2008a) Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J Biomol NMR 40(2):107-119. doi:10.1007/s10858- 007-9214-2
    • (2008) J Biomol NMR , vol.40 , Issue.2 , pp. 107-119
    • D'auvergne, E.J.1    Gooley, P.R.2
  • 9
    • 38349050193 scopus 로고    scopus 로고
    • Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor
    • doi:10.1007/s10858-007.9213-3
    • d'Auvergne EJ, Gooley PR (2008b) Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J Biomol NMR 40(2):121-133. doi:10.1007/s10858-007-9213-3
    • (2008) J Biomol NMR 40 , vol.2 , pp. 121-133
    • D'auvergne, E.J.1    Gooley, P.R.2
  • 10
    • 0034048847 scopus 로고    scopus 로고
    • Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data
    • DOI 10.1023/A:1008305808620
    • Dosset P, Hus JC, Blackledge M, Marion D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16(1):23-28 (Pubitemid 30114721)
    • (2000) Journal of Biomolecular NMR , vol.16 , Issue.1 , pp. 23-28
    • Dosset, P.1    Hus, J.-C.2    Blackledge, M.3    Marion, D.4
  • 11
    • 77249152215 scopus 로고    scopus 로고
    • TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance
    • doi: 10.1016/j.bpj.2009.08.061
    • Fisette O, Morin S, Savard PY, Lague P, Gagne SM (2010) TEM-1 backbone dynamics-insights from combined molecular dynamics and nuclear magnetic resonance. Biophys J 98(4):637-645. doi: 10.1016/j.bpj.2009.08.061
    • (2010) Biophys J , vol.98 , Issue.4 , pp. 637-645
    • Fisette, O.1    Morin, S.2    Savard, P.Y.3    Lague, P.4    Gagne, S.M.5
  • 12
    • 0031566963 scopus 로고    scopus 로고
    • 15N relaxation with monomer/dimer equilibration
    • DOI 10.1006/jmbi.1996.0771
    • Fushman D, Cahill S, Cowburn D (1997) The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration. J Mol Biol 266(1):173-194. doi:10.1006/jmbi.1996.0771 (Pubitemid 27170527)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.1 , pp. 173-194
    • Fushman, D.1    Cahill, S.2    Cowburn, D.3
  • 13
    • 22244486997 scopus 로고    scopus 로고
    • 15N NMR relaxation measurements
    • DOI 10.1021/bi050149t
    • Gitti RK, Wright NT, Margolis JW, Varney KM, Weber DJ, Margolis FL (2005) Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements. Biochemistry 44(28):9673-9679. doi:10.1021/bi050149t (Pubitemid 40994361)
    • (2005) Biochemistry , vol.44 , Issue.28 , pp. 9673-9679
    • Gitti, R.K.1    Wright, N.T.2    Margolis, J.W.3    Varney, K.M.4    Weber, D.J.5    Margolis, F.L.6
  • 14
    • 0004757060 scopus 로고    scopus 로고
    • University of California, San Francisco
    • Goddard TD, Kneller DG (2006) Sparky 3. University of California, San Francisco
    • (2006) Sparky , vol.3
    • Goddard, T.D.1    Kneller, D.G.2
  • 15
    • 77951270272 scopus 로고    scopus 로고
    • Large conformational changes in proteins: Signaling and other functions
    • doi:10.1016/j.sbi.2009.12.004
    • Grant BJ, Gorfe AA, McCammon JA (2010) Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol 20(2):142-147. doi:10.1016/j.sbi.2009.12.004
    • (2010) Curr Opin Struct Biol , vol.20 , Issue.2 , pp. 142-147
    • Grant, B.J.1    Gorfe, A.A.2    McCammon, J.A.3
  • 16
    • 0037649010 scopus 로고    scopus 로고
    • 15N CSA/dipolar relaxation interference from coupled HSQC spectra
    • DOI 10.1023/A:1023546107553
    • Hall JB, Dayie KT, Fushman D (2003) Direct measurement of the 15N CSA/dipolar relaxation interference from coupled HSQC spectra. J Biomol NMR 26(2):181-186 (Pubitemid 36609050)
    • (2003) Journal of Biomolecular NMR , vol.26 , Issue.2 , pp. 181-186
    • Hall, J.B.1    Dayie, K.T.2    Fushman, D.3
  • 17
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
    • DOI 10.1021/cr040422h
    • Igumenova TI, Frederick KK, Wand AJ (2006) Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 106(5):1672-1699. doi: 10.1021/cr040422h (Pubitemid 43792776)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1672-1699
    • Igumenova, T.I.1    Frederick, K.K.2    Wand, A.J.3
  • 18
    • 33646911358 scopus 로고    scopus 로고
    • Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences
    • DOI 10.1021/cr040421p
    • Jarymowycz VA, Stone MJ (2006) Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem Rev 106(5):1624-1671. doi: 10.1021/cr040421p (Pubitemid 43792775)
    • (2006) Chemical Reviews , vol.106 , Issue.5 , pp. 1624-1671
    • Jarymowycz, V.A.1    Stone, M.J.2
  • 20
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results
    • Lipari G, Szabo A (1982a) Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results. J Am Chem Soc 104(17): 4559-4570
    • (1982) J Am Chem Soc , vol.104 , Issue.17 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 21
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic-resonance relaxation of macromolecules. Theory and range of validity
    • Lipari G, Szabo A (1982b) Model-free approach to the interpretation of nuclear magnetic-resonance relaxation of macromolecules. Theory and range of validity. J Am Chem Soc 104(17): 4546-4559
    • (1982) J Am Chem Soc , vol.104 , Issue.17 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 22
    • 0028941877 scopus 로고
    • Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme
    • Mandel AM, Akke M, Palmer AG 3rd (1995) Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 246(1):144-163
    • (1995) J Mol Biol , vol.246 , Issue.1 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer Iii, A.G.3
  • 23
    • 68949086333 scopus 로고    scopus 로고
    • NMR dynamics of PSE-4 beta-lactamase: An interplay of ps-ns order and mus-ms motions in the active site
    • doi:10.1016/j.bpj.2009.02.068
    • Morin S, Gagne SM (2009) NMR dynamics of PSE-4 beta-lactamase: an interplay of ps-ns order and mus-ms motions in the active site. Biophys J 96(11):4681-4691. doi:10.1016/j.bpj.2009.02.068
    • (2009) Biophys J , vol.96 , Issue.11 , pp. 4681-4691
    • Morin, S.1    Gagne, S.M.2
  • 24
    • 12044256620 scopus 로고
    • Intramolecular Motions of a zinc finger DNA-binding domain from XFIN characterized by proton-detected natural abundance C-12 heteronuclear NMRspectroscopy
    • Palmer AG, Rance M, Wright PE (1991) Intramolecular Motions of a zinc finger DNA-binding domain from XFIN characterized by proton-detected natural abundance C-12 heteronuclear NMRspectroscopy. J Am Chem Soc 113(12):4371-4380
    • (1991) J Am Chem Soc , vol.113 , Issue.12 , pp. 4371-4380
    • Palmer, A.G.1    Rance, M.2    Wright, P.E.3
  • 25
    • 78149500243 scopus 로고    scopus 로고
    • Using NMR to study fast dynamics in proteins: Methods and applications
    • doi:10.1016/j.coph.2010.09.006
    • Sapienza PJ, Lee AL (2010) Using NMR to study fast dynamics in proteins: methods and applications. Curr Opin Pharmacol 10(6):723-730. doi:10.1016/j.coph.2010.09.006
    • (2010) Curr Opin Pharmacol , vol.10 , Issue.6 , pp. 723-730
    • Sapienza, P.J.1    Lee, A.L.2
  • 26
    • 67650450454 scopus 로고    scopus 로고
    • Functional aspects of protein flexibility
    • doi: 10.1007/s00018-009-0014-6
    • Teilum K, Olsen JG, Kragelund BB (2009) Functional aspects of protein flexibility. Cell Mol Life Sci 66(14):2231-2247. doi: 10.1007/s00018-009-0014-6
    • (2009) Cell Mol Life Sci , vol.66 , Issue.14 , pp. 2231-2247
    • Teilum, K.1    Olsen, J.G.2    Kragelund, B.B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.