메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Robust probabilistic superposition and comparison of protein structures

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL EXPRESSIONS; CONFORMATIONAL DIFFERENCES; DISSIMILARITY MEASURES; EXPECTATION-MAXIMIZATION ALGORITHMS; HEAVY-TAILED DISTRIBUTION; PROTEIN STRUCTURE COMPARISON; ROOT MEAN SQUARE DEVIATIONS; STRUCTURAL BIOINFORMATICS;

EID: 77954054037     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-363     Document Type: Article
Times cited : (12)

References (45)
  • 1
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • 10.1093/nar/26.18.4280, 147832, 9722650
    • Gerstein M, Krebs W. A database of macromolecular motions. Nucleic Acids Res 1998, 26:4280-4290. 10.1093/nar/26.18.4280, 147832, 9722650.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 2
    • 1042275603 scopus 로고    scopus 로고
    • Exploring the range of protein flexibility, from a structural proteomics perspective
    • 10.1016/j.cbpa.2003.12.006, 15036151
    • Gerstein M, Echols N. Exploring the range of protein flexibility, from a structural proteomics perspective. Curr Opin Chem Biol 2004, 8:14-19. 10.1016/j.cbpa.2003.12.006, 15036151.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 14-19
    • Gerstein, M.1    Echols, N.2
  • 3
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanisms of signal transduction
    • 10.1126/science.1108595, 15933191
    • Changeux JP, Edelstein SJ. Allosteric mechanisms of signal transduction. Science 2005, 308:1424-1428. 10.1126/science.1108595, 15933191.
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.P.1    Edelstein, S.J.2
  • 4
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • 10.1110/ps.03259908, 2492820, 18560010
    • Cui Q, Karplus M. Allostery and cooperativity revisited. Protein Sci 2008, 17:1295-1307. 10.1110/ps.03259908, 2492820, 18560010.
    • (2008) Protein Sci , vol.17 , pp. 1295-1307
    • Cui, Q.1    Karplus, M.2
  • 5
    • 0032584781 scopus 로고    scopus 로고
    • Recommendations for the presentation of NMR structures of proteins and nucleic acids
    • 10.1006/jmbi.1998.1852, 9671561
    • Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE, Wüthrich K. Recommendations for the presentation of NMR structures of proteins and nucleic acids. J Mol Biol 1998, 280(5):933-952. 10.1006/jmbi.1998.1852, 9671561.
    • (1998) J Mol Biol , vol.280 , Issue.5 , pp. 933-952
    • Markley, J.L.1    Bax, A.2    Arata, Y.3    Hilbers, C.W.4    Kaptein, R.5    Sykes, B.D.6    Wright, P.E.7    Wüthrich, K.8
  • 6
    • 0033505579 scopus 로고    scopus 로고
    • Rotational superposition: a review of methods
    • Flower DR. Rotational superposition: a review of methods. J Mol Graph Model 1999, 17:238-244.
    • (1999) J Mol Graph Model , vol.17 , pp. 238-244
    • Flower, D.R.1
  • 7
    • 9244238239 scopus 로고
    • A mathematical model-building procedure for proteins
    • Diamond R. A mathematical model-building procedure for proteins. Acta Crystallographica 1966, 21(2):253-266.
    • (1966) Acta Crystallographica , vol.21 , Issue.2 , pp. 253-266
    • Diamond, R.1
  • 8
    • 0000408083 scopus 로고
    • A mathematical procedure for superimposing atomic coordinates of proteins
    • McLachlan AD. A mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallographica Section A 1972, 28(6):656-657.
    • (1972) Acta Crystallographica Section A , vol.28 , Issue.6 , pp. 656-657
    • McLachlan, A.D.1
  • 9
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Cryst 1976, A32:922-923.
    • (1976) Acta Cryst , vol.A , Issue.32 , pp. 922-923
    • Kabsch, W.1
  • 10
    • 0002404088 scopus 로고
    • On the orthogonal transformation used for structural comparisons
    • Kearsley SK. On the orthogonal transformation used for structural comparisons. Acta Crystallographica Section A 1989, 45(2):208-210.
    • (1989) Acta Crystallographica Section A , vol.45 , Issue.2 , pp. 208-210
    • Kearsley, S.K.1
  • 11
    • 84888276663 scopus 로고    scopus 로고
    • Fast determination of the optimal rotational matrix for macromolecular superpositions
    • Liu P, Agrafiotis DK, Theobald DL. Fast determination of the optimal rotational matrix for macromolecular superpositions. J Comput Chem 2009,
    • (2009) J Comput Chem
    • Liu, P.1    Agrafiotis, D.K.2    Theobald, D.L.3
  • 12
    • 36149010019 scopus 로고
    • Some Studies Concerning Rotating Axes and Polyatomic Molecules
    • Eckart C. Some Studies Concerning Rotating Axes and Polyatomic Molecules. Phys Rev 1935, 47(7):552-558.
    • (1935) Phys Rev , vol.47 , Issue.7 , pp. 552-558
    • Eckart, C.1
  • 13
    • 20544436144 scopus 로고    scopus 로고
    • Eckart axis conditions and the minimization of the root-mean-square deviation: two closely related problems
    • 10.1063/1.1929739, 15974649
    • Kudin KN, Dymarsky AY. Eckart axis conditions and the minimization of the root-mean-square deviation: two closely related problems. J Chem Phys 2005, 122:224105. 10.1063/1.1929739, 15974649.
    • (2005) J Chem Phys , vol.122 , pp. 224105
    • Kudin, K.N.1    Dymarsky, A.Y.2
  • 14
    • 44349129711 scopus 로고    scopus 로고
    • Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures
    • 10.1063/1.2902290, 18500850
    • Kneller GR. Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures. J Chem Phys 2008, 128:194101. 10.1063/1.2902290, 18500850.
    • (2008) J Chem Phys , vol.128 , pp. 194101
    • Kneller, G.R.1
  • 15
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
    • 10.1016/S0969-2126(96)00018-4, 8805521
    • Müller CW, Schlauderer GJ, Reinstein J, Schulz GE. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 1996, 4:147-156. 10.1016/S0969-2126(96)00018-4, 8805521.
    • (1996) Structure , vol.4 , pp. 147-156
    • Müller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 16
    • 0032533403 scopus 로고    scopus 로고
    • Extraction of geometrically similar substructures: least-squares and Chebyshev fitting and the difference distance matrix
    • 10.1002/(SICI)1097-0134(19981115)33:3<320::AID-PROT2>3.0.CO;2-Q, 9829692
    • Lesk AM. Extraction of geometrically similar substructures: least-squares and Chebyshev fitting and the difference distance matrix. Proteins 1998, 33:320-328. 10.1002/(SICI)1097-0134(19981115)33:3<320::AID-PROT2>3.0.CO;2-Q, 9829692.
    • (1998) Proteins , vol.33 , pp. 320-328
    • Lesk, A.M.1
  • 17
    • 60649092330 scopus 로고    scopus 로고
    • Using least median of squares for structural superposition of flexible proteins
    • 10.1186/1471-2105-10-29, 2639377, 19159484
    • Liu YS, Fang Y, Ramani K. Using least median of squares for structural superposition of flexible proteins. BMC Bioinformatics 2009, 10:29. 10.1186/1471-2105-10-29, 2639377, 19159484.
    • (2009) BMC Bioinformatics , vol.10 , pp. 29
    • Liu, Y.S.1    Fang, Y.2    Ramani, K.3
  • 18
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, 19(Suppl 2):i246-255.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 19
    • 45949117843 scopus 로고
    • A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data
    • Nilges M, Clore GM, Gronenborn AM. A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data. FEBS Lett 1987, 219:17-21.
    • (1987) FEBS Lett , vol.219 , pp. 17-21
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 21
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: application to the immunoglobulins
    • 10.1006/jmbi.1995.0423, 7643385
    • Gerstein M, Altman RB. Average core structures and variability measures for protein families: application to the immunoglobulins. J Mol Biol 1995, 251:161-175. 10.1006/jmbi.1995.0423, 7643385.
    • (1995) J Mol Biol , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 22
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J, 9294863
    • Wriggers W, Schulten K. Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 1997, 29:1-14. 10.1002/(SICI)1097-0134(199709)29:1<1::AID-PROT1>3.0.CO;2-J, 9294863.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 23
    • 18844415920 scopus 로고    scopus 로고
    • Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
    • Snyder DA, Montelione GT. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins Struct Funct Bioinf 2005, 59(4):673-686.
    • (2005) Proteins Struct Funct Bioinf , vol.59 , Issue.4 , pp. 673-686
    • Snyder, D.A.1    Montelione, G.T.2
  • 24
    • 33744807436 scopus 로고    scopus 로고
    • Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures
    • 10.1529/biophysj.105.066654, 1471868, 16565070
    • Damm KL, Carlson HA. Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures. Biophys J 2006, 90(12):4558-4573. 10.1529/biophysj.105.066654, 1471868, 16565070.
    • (2006) Biophys J , vol.90 , Issue.12 , pp. 4558-4573
    • Damm, K.L.1    Carlson, H.A.2
  • 25
    • 84888279153 scopus 로고    scopus 로고
    • Superimposition of protein structures with dynamically weighted RMSD
    • Wu D, Wu Z. Superimposition of protein structures with dynamically weighted RMSD. J Mol Model 2009,
    • (2009) J Mol Model
    • Wu, D.1    Wu, Z.2
  • 26
    • 0001962564 scopus 로고    scopus 로고
    • The molecular modeling toolkit: A new approach to molecular simulations
    • Hinsen K. The molecular modeling toolkit: A new approach to molecular simulations. J Comp Chem 2000, 9:79-85.
    • (2000) J Comp Chem , vol.9 , pp. 79-85
    • Hinsen, K.1
  • 28
    • 0003071947 scopus 로고
    • Scale mixtures of normal distributions
    • Andrews D, Mallows C. Scale mixtures of normal distributions. J Royal Stat Soc 1974, 36:99-102.
    • (1974) J Royal Stat Soc , vol.36 , pp. 99-102
    • Andrews, D.1    Mallows, C.2
  • 29
    • 0039713775 scopus 로고
    • On scale mixtures of normal distributions
    • West M. On scale mixtures of normal distributions. Biometrika 1987, 74:646-648.
    • (1987) Biometrika , vol.74 , pp. 646-648
    • West, M.1
  • 31
    • 33748683496 scopus 로고    scopus 로고
    • Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem
    • 10.1073/pnas.0508445103, 1664551, 17130458
    • Theobald DL, Wuttke DS. Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem. Proc Natl Acad Sci USA 2006, 103(49):18521-18527. 10.1073/pnas.0508445103, 1664551, 17130458.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.49 , pp. 18521-18527
    • Theobald, D.L.1    Wuttke, D.S.2
  • 32
    • 0028885711 scopus 로고
    • Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution
    • 10.1038/nsb1295-1083, 8846220
    • Braig K, Adams PD, Brünger AT. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat Struct Biol 1995, 2(12):1083-1094. 10.1038/nsb1295-1083, 8846220.
    • (1995) Nat Struct Biol , vol.2 , Issue.12 , pp. 1083-1094
    • Braig, K.1    Adams, P.D.2    Brünger, A.T.3
  • 33
    • 0030870719 scopus 로고    scopus 로고
    • The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex
    • 10.1038/41944, 9285585
    • Xu Z, Horwich AL, Sigler PB. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 1997, 388(6644):741-750. 10.1038/41944, 9285585.
    • (1997) Nature , vol.388 , Issue.6644 , pp. 741-750
    • Xu, Z.1    Horwich, A.L.2    Sigler, P.B.3
  • 34
    • 17444405610 scopus 로고    scopus 로고
    • Structural basis of pore formation by the bacterial toxin pneumolysin
    • 10.1016/j.cell.2005.02.033, 15851031
    • Tilley SJ, Orlova EV, Gilbert RJC, Andrew PW, Saibil HR. Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 2005, 121(2):247-256. 10.1016/j.cell.2005.02.033, 15851031.
    • (2005) Cell , vol.121 , Issue.2 , pp. 247-256
    • Tilley, S.J.1    Orlova, E.V.2    Gilbert, R.J.C.3    Andrew, P.W.4    Saibil, H.R.5
  • 35
    • 0022429234 scopus 로고
    • An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution
    • 10.1016/0022-2836(85)90346-8, 2582141
    • Havel TF, Wüthrich K. An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J Mol Biol 1985, 182:281-294. 10.1016/0022-2836(85)90346-8, 2582141.
    • (1985) J Mol Biol , vol.182 , pp. 281-294
    • Havel, T.F.1    Wüthrich, K.2
  • 36
    • 0029159794 scopus 로고
    • Solution structure of calcium-free calmodulin
    • 10.1038/nsb0995-768, 7552748
    • Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A. Solution structure of calcium-free calmodulin. Nat Struct Biol 1995, 2(9):768-776. 10.1038/nsb0995-768, 7552748.
    • (1995) Nat Struct Biol , vol.2 , Issue.9 , pp. 768-776
    • Kuboniwa, H.1    Tjandra, N.2    Grzesiek, S.3    Ren, H.4    Klee, C.B.5    Bax, A.6
  • 38
  • 41
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm (with discussion)
    • Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Stat Soc B 1977, 39:1-38.
    • (1977) J R Stat Soc B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 42
    • 0021518209 scopus 로고
    • Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
    • Geman S, Geman D. Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images. IEEE Trans PAMI 1984, 6(6):721-741.
    • (1984) IEEE Trans PAMI , vol.6 , Issue.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 44
    • 70449521305 scopus 로고    scopus 로고
    • Generation of three-dimensional random rotations in fitting and matching problems
    • Habeck M. Generation of three-dimensional random rotations in fitting and matching problems. Computational Statistics 2009, 24:719-731.
    • (2009) Computational Statistics , vol.24 , pp. 719-731
    • Habeck, M.1
  • 45
    • 0000324169 scopus 로고
    • Adaptive Rejection Sampling for Gibbs Sampling
    • Gilks WR, Wild P. Adaptive Rejection Sampling for Gibbs Sampling. Applied Statistics 1992, 41(2):337-348.
    • (1992) Applied Statistics , vol.41 , Issue.2 , pp. 337-348
    • Gilks, W.R.1    Wild, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.