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Volumn 75, Issue 1, 2009, Pages 206-216

COCO: A simple tool to enrich the representation of conformational variability in NMR structures

Author keywords

Amyloid beta peptide; Beetle antifreeze protein; Calmodulin; Essential dynamics; Moth chemosensory protein; Principal component analysis; RECOORD

Indexed keywords

AMYLOID BETA PROTEIN[25-35]; ANTIFREEZE PROTEIN; CALMODULIN; CHEMOSENSORY PROTEIN; PROTEIN DERIVATIVE; UNCLASSIFIED DRUG;

EID: 65249112821     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22235     Document Type: Article
Times cited : (17)

References (32)
  • 1
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 2007;35:D301-D303.
    • (2007) Nucleic Acids Res , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 4
    • 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. The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR 2007;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
  • 5
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W, Habeck M, Nilges M. Inferential structure determination. Science 2005;309:303-306.
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 8
    • 34248159870 scopus 로고    scopus 로고
    • Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
    • Rueda M, Chacon P, Orozco M. Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure 2007;15:565-575.
    • (2007) Structure , vol.15 , pp. 565-575
    • Rueda, M.1    Chacon, P.2    Orozco, M.3
  • 9
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001; 115:6289-6292.
    • (2001) J Chem Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Karplus, M.2
  • 10
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance-matrix
    • Schlitter J. Estimation of absolute and relative entropies of macromolecules using the covariance-matrix. Chem Phys Lett 1993;215: 617-621.
    • (1993) Chem Phys Lett , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 11
    • 0032101346 scopus 로고    scopus 로고
    • Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
    • Abseher R, Horstink L, Hilbers CW, Nilges M. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins 1998;31:370-382.
    • (1998) Proteins , vol.31 , pp. 370-382
    • Abseher, R.1    Horstink, L.2    Hilbers, C.W.3    Nilges, M.4
  • 12
    • 0034057133 scopus 로고    scopus 로고
    • Unraveling the symmetry ambiguity in a hexamer: Calculation of the R-6 human insulin structure
    • O'Donoghue SI, Chang XQ, Abseher R, Nilges M, Led JJ. Unraveling the symmetry ambiguity in a hexamer: calculation of the R-6 human insulin structure. J Biomol NMR 2000;16:93-108.
    • (2000) J Biomol NMR , vol.16 , pp. 93-108
    • O'Donoghue, S.I.1    Chang, X.Q.2    Abseher, R.3    Nilges, M.4    Led, J.J.5
  • 13
    • 25144437529 scopus 로고    scopus 로고
    • Dynamite extended: Two new services to simplify protein dynamic analysis
    • Barrett CP, Noble MEM. Dynamite extended: two new services to simplify protein dynamic analysis. Bioinformatics 2005;21:3174-3175.
    • (2005) Bioinformatics , vol.21 , pp. 3174-3175
    • Barrett, C.P.1    Noble, M.E.M.2
  • 15
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek ST, Clark TW, Scott LR, McCammon JA. Molecular dynamics of acetylcholinesterase dimer complexed with tacrine. J Am Chem Soc 1997;119:9513-9522.
    • (1997) J Am Chem Soc , vol.119 , pp. 9513-9522
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 16
    • 21644440760 scopus 로고    scopus 로고
    • Statistical analysis on high-dimensional spheres and shape spaces
    • Dryden IL. Statistical analysis on high-dimensional spheres and shape spaces. Annals Stat 2005;33:1643-1665.
    • (2005) Annals Stat , vol.33 , pp. 1643-1665
    • Dryden, I.L.1
  • 18
    • 0031453963 scopus 로고    scopus 로고
    • OLDERADO: On-line database of ensemble representatives and domains
    • Kelley LA, Sutcliffe MJ. OLDERADO: on-line database of ensemble representatives and domains. Protein Sci 1997;6:2628-2630.
    • (1997) Protein Sci , vol.6 , pp. 2628-2630
    • Kelley, L.A.1    Sutcliffe, M.J.2
  • 22
    • 0032483035 scopus 로고    scopus 로고
    • Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?
    • Coles M, Bicknell W, Watson AA, Fairlie DP, Craik DJ. Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is? Biochemistry 1998;37:11064-11077.
    • (1998) Biochemistry , vol.37 , pp. 11064-11077
    • Coles, M.1    Bicknell, W.2    Watson, A.A.3    Fairlie, D.P.4    Craik, D.J.5
  • 26
    • 0022931544 scopus 로고
    • A model for the Ca-2+-induced conformational transition of troponin-C - a trigger for muscle-contraction
    • Herzberg O, Moult J, James MNG. A model for the Ca-2+-induced conformational transition of troponin-C - a trigger for muscle-contraction. J Biol Chem 1986;261:2638-2644.
    • (1986) J Biol Chem , vol.261 , pp. 2638-2644
    • Herzberg, O.1    Moult, J.2    James, M.N.G.3
  • 27
    • 0033527588 scopus 로고    scopus 로고
    • Structural dynamics in the C-terminal domain of calmodulin at low calcium levels
    • Malmendal A, Evenaés J, Forseån S, Akke M. Structural dynamics in the C-terminal domain of calmodulin at low calcium levels. J Mol Biol 1999;93:883-899.
    • (1999) J Mol Biol , vol.93 , pp. 883-899
    • Malmendal, A.1    Evenaés, J.2    Forseån, S.3    Akke, M.4
  • 28
    • 0029005929 scopus 로고
    • Rotational dynamics of calcium-free calmodulin studied by 15N relaxation measurements
    • Tjandra N, Kuboniwa H, Ren H, Bax A. Rotational dynamics of calcium-free calmodulin studied by 15N relaxation measurements. Eur J Biochem 1995;230:1014-1024.
    • (1995) Eur J Biochem , vol.230 , pp. 1014-1024
    • Tjandra, N.1    Kuboniwa, H.2    Ren, H.3    Bax, A.4
  • 30
    • 18844433630 scopus 로고    scopus 로고
    • Assessing precision and accuracy of protein structures derived from NMR data
    • Snyder DA, Bhattacharya A, Huang YJ, Montelione GT. Assessing precision and accuracy of protein structures derived from NMR data. Proteins 2005;59:655-661.
    • (2005) Proteins , vol.59 , pp. 655-661
    • Snyder, D.A.1    Bhattacharya, A.2    Huang, Y.J.3    Montelione, G.T.4
  • 31
    • 33645790319 scopus 로고    scopus 로고
    • Traditional biomolecular structure determination by NMR spectroscopy allows for major errors
    • Nabuurs SB, Spronk CAEM, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol 2006;2:71-79.
    • (2006) PLoS Comput Biol , vol.2 , pp. 71-79
    • Nabuurs, S.B.1    Spronk, C.A.E.M.2    Vuister, G.W.3    Vriend, G.4
  • 32
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.