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Volumn 24, Issue 2-3, 2005, Pages 165-182

A probability-based similarity measure for saupe alignment tensors with applications to residual dipolar couplings in NMR structural biology

Author keywords

Alignment tensor; NMR structural biology; Orthogonal image; Residual dipolar couplings; Rotations; Saupe matrix; SO (3); Subgroup method

Indexed keywords

ALGORITHMS; BIOLOGY; EIGENVALUES AND EIGENFUNCTIONS; FREQUENCIES; GENES; MATRIX ALGEBRA; NUCLEAR MAGNETIC RESONANCE; PROBABILITY; PROTEINS; X RAY CRYSTALLOGRAPHY;

EID: 13444283602     PISSN: 02783649     EISSN: None     Source Type: Journal    
DOI: 10.1177/0278364905050351     Document Type: Article
Times cited : (6)

References (53)
  • 1
    • 0036008211 scopus 로고    scopus 로고
    • Residual dipolar couplings: Synergy between NMR and structural genomics
    • Al-Hashimi, H. M., and Patel, D. J. 2002. Residual dipolar couplings: synergy between NMR and structural genomics. Journal of Biomolecular NMR 22(1):18.
    • (2002) Journal of Biomolecular NMR , vol.22 , Issue.1 , pp. 18
    • Al-Hashimi, H.M.1    Patel, D.J.2
  • 2
    • 0036306532 scopus 로고    scopus 로고
    • Towards structural genomics of RNA: Rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings
    • Al-Hashimi, H. M., Gorin, A., Majumdar, A., Gosser, Y., and Patel, D. J. 2002. Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings. Journal of Molecular Biology 318:637-649.
    • (2002) Journal of Molecular Biology , vol.318 , pp. 637-649
    • Al-Hashimi, H.M.1    Gorin, A.2    Majumdar, A.3    Gosser, Y.4    Patel, D.J.5
  • 3
    • 0035695158 scopus 로고    scopus 로고
    • Protein backbone structure determination using only residual dipolar couplings from one ordering medium
    • Andrec, M., Du, P., and Levy, R. M. 2001. Protein backbone structure determination using only residual dipolar couplings from one ordering medium. Journal of Biomolecular NMR 21:335-347.
    • (2001) Journal of Biomolecular NMR , vol.21 , pp. 335-347
    • Andrec, M.1    Du, P.2    Levy, R.M.3
  • 4
    • 0001439567 scopus 로고
    • The structures of the monoclinic and orthorhombic forms of hen egg-white lysozyme at 6 angstroms resolution
    • Artymiuk, P. J., Blake, C. C. F., Rice, D. W., and Wilson, K. S. 1982. The structures of the monoclinic and orthorhombic forms of hen egg-white lysozyme at 6 angstroms resolution. Acta Crystallographica B 38:778.
    • (1982) Acta Crystallographica B , vol.38 , pp. 778
    • Artymiuk, P.J.1    Blake, C.C.F.2    Rice, D.W.3    Wilson, K.S.4
  • 5
    • 0034824952 scopus 로고    scopus 로고
    • Validation of protein structure from preparations of encapsulated proteins dissolved in low viscosity fluids
    • Babu, C. R., Flynn, P. F., and Wand, A. J. 2001. Validation of protein structure from preparations of encapsulated proteins dissolved in low viscosity fluids. Journal of the American Chemical Society 123:2691.
    • (2001) Journal of the American Chemical Society , vol.123 , pp. 2691
    • Babu, C.R.1    Flynn, P.F.2    Wand, A.J.3
  • 7
    • 0027434240 scopus 로고
    • Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglc
    • Chen, Y., Reizer, J., Saier M. H. Jr, Fairbrother, W. J., and Wright, P. E. 1993. Mapping of the binding interfaces of the proteins of the bacterial phosphotransferase system, HPr and IIAglc. Biochemistry 32(1):32-37.
    • (1993) Biochemistry , vol.32 , Issue.1 , pp. 32-37
    • Chen, Y.1    Reizer, J.2    Saier Jr., M.H.3    Fairbrother, W.J.4    Wright, P.E.5
  • 8
    • 0032113480 scopus 로고    scopus 로고
    • A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information
    • Clore, G. M., Gronenborn, A. M., and Bax, A. 1998. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. Journal of Magnetic Resonance 133:216-221.
    • (1998) Journal of Magnetic Resonance , vol.133 , pp. 216-221
    • Clore, G.M.1    Gronenborn, A.M.2    Bax, A.3
  • 9
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • Cornilescu, G., Marquardt, J. L., Ottiger, M., and Bax, A. 1998. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. Journal of the American Chemical Society 120:6836-6837.
    • (1998) Journal of the American Chemical Society , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 10
    • 0034620764 scopus 로고    scopus 로고
    • Protein structure determination using molecular fragment replacement and NMR dipolar couplings
    • Delaglio, F., Kontaxis, G., and Bax, A. 2000. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. Journal of the American Chemical Society 122:2142-2143.
    • (2000) Journal of the American Chemical Society , vol.122 , pp. 2142-2143
    • Delaglio, F.1    Kontaxis, G.2    Bax, A.3
  • 12
    • 0015994218 scopus 로고
    • Real-space refinement of the structure of hen egg-white lysozyme
    • Diamond, R. 1974. Real-space refinement of the structure of hen egg-white lysozyme. Journal of Molecular Biology 82:371-391.
    • (1974) Journal of Molecular Biology , vol.82 , pp. 371-391
    • Diamond, R.1
  • 16
    • 0028354429 scopus 로고
    • Two crystal structures of the B1 immunoglobulinbinding domain of streptococcal protein G and comparison with NMR
    • Gallagher, T., Alexander, P., Bryan, P., and Gilliland, G. L. 1994. Two crystal structures of the B1 immunoglobulinbinding domain of streptococcal protein G and comparison with NMR. Biochemistry 33:4721-4729.
    • (1994) Biochemistry , vol.33 , pp. 4721-4729
    • Gallagher, T.1    Alexander, P.2    Bryan, P.3    Gilliland, G.L.4
  • 17
    • 0037269913 scopus 로고    scopus 로고
    • Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints
    • Giesen, A. W., Homans, S. W., and Brown, J. M. 2003. Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints. Journal of Biomolecular NMR 25(1):63-71.
    • (2003) Journal of Biomolecular NMR , vol.25 , Issue.1 , pp. 63-71
    • Giesen, A.W.1    Homans, S.W.2    Brown, J.M.3
  • 18
    • 0036006752 scopus 로고    scopus 로고
    • Gd-HPDO3A, a complex to obtain high-phasing-power heavy atom derivatives for SAD and MAD experiments: Results with tetragonal hen egg-white lysozyme
    • Girard, E., Chantalat, L., Vicat, J., and Kahn, R. 2001. Gd-HPDO3A, a complex to obtain high-phasing-power heavy atom derivatives for SAD and MAD experiments: results with tetragonal hen egg-white lysozyme. Acta Crystallographica D 58:1-9.
    • (2001) Acta Crystallographica D , vol.58 , pp. 1-9
    • Girard, E.1    Chantalat, L.2    Vicat, J.3    Kahn, R.4
  • 21
    • 2442528145 scopus 로고
    • Distance metrics for comparing shapes in the plane
    • Chapter 8, B. R. Donald, D. Kapur, and J. Mundy, editors. Academic Press, Harcourt Jovanovich, London
    • Huttenlocher, D. P., and Kedem, K. 1992. Distance metrics for comparing shapes in the plane. Symbolic and Numerical Computation for Artificial Intelligence, Chapter 8, B. R. Donald, D. Kapur, and J. Mundy, editors. Academic Press, Harcourt Jovanovich, London, pp. 201-219.
    • (1992) Symbolic and Numerical Computation for Artificial Intelligence , pp. 201-219
    • Huttenlocher, D.P.1    Kedem, K.2
  • 23
    • 0033566738 scopus 로고    scopus 로고
    • Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin
    • Johnson, E. C., Lazar, G. A., Desjarlais, J. R., and Handel, T. M. 1999. Solution structure and dynamics of a designed hydrophobic core variant of ubiquitin. Structure 7(8):967-976.
    • (1999) Structure , vol.7 , Issue.8 , pp. 967-976
    • Johnson, E.C.1    Lazar, G.A.2    Desjarlais, J.R.3    Handel, T.M.4
  • 25
    • 85069106767 scopus 로고
    • Miscellany
    • chapter 10. Springer-Verlag, Berlin
    • Kinsey, L. C. 1991. Miscellany. Topology of Surfaces, chapter 10. Springer-Verlag, Berlin, pp. 199-203.
    • (1991) Topology of Surfaces , pp. 199-203
    • Kinsey, L.C.1
  • 26
    • 0029140564 scopus 로고
    • The influence of temperature on lysozyme crystals - Structure and dynamics of protein and water
    • Kurinov, I. V., and Harrison, R. W. 1995. The influence of temperature on lysozyme crystals - structure and dynamics of protein and water. Acta Crystallographica D 51:98-109.
    • (1995) Acta Crystallographica D , vol.51 , pp. 98-109
    • Kurinov, I.V.1    Harrison, R.W.2
  • 27
    • 0033577269 scopus 로고    scopus 로고
    • Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration
    • Kuszewski, J., Gronenborn, A. M., and Clore, G. M. 1999. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. Journal of the American Chemistry Society 121:2337-2338.
    • (1999) Journal of the American Chemistry Society , vol.121 , pp. 2337-2338
    • Kuszewski, J.1    Gronenborn, A.M.2    Clore, G.M.3
  • 28
    • 1842555458 scopus 로고    scopus 로고
    • An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments
    • Langmead, C. J., and Donald, B. R. 2004. An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. Journal of Biomolecular NMR 29(2):111-138.
    • (2004) Journal of Biomolecular NMR , vol.29 , Issue.2 , pp. 111-138
    • Langmead, C.J.1    Donald, B.R.2
  • 30
    • 3142588772 scopus 로고    scopus 로고
    • A polynomial time nuclear vector replacement algorithm for automated NMR resonance assign ments
    • Langmead, C. J., Yan, A. K., Wang, L., Lilien, R., and Donald, B. R. 2004. A polynomial time nuclear vector replacement algorithm for automated NMR resonance assign ments. Journal of Computational Biology 11(2-3):277-298.
    • (2004) Journal of Computational Biology , vol.11 , Issue.2-3 , pp. 277-298
    • Langmead, C.J.1    Yan, A.K.2    Wang, L.3    Lilien, R.4    Donald, B.R.5
  • 32
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • Losonczi, J. A., Andrec, M., Fischer, W. F., and Prestegard, J. H. 1999. Order matrix analysis of residual dipolar couplings using singular value decomposition. Journal of Magnetic Resonance 138(2):334-342.
    • (1999) Journal of Magnetic Resonance , vol.138 , Issue.2 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, W.F.3    Prestegard, J.H.4
  • 34
    • 85069110798 scopus 로고    scopus 로고
    • The orthogonal image method for generating uniform distributions of rotation matrices
    • submitted for publication
    • Mitchell, J. C. 2004. The orthogonal image method for generating uniform distributions of rotation matrices. Proteins: Structure, Function and Genetics submitted for publication.
    • (2004) Proteins: Structure, Function and Genetics
    • Mitchell, J.C.1
  • 36
    • 0032925243 scopus 로고    scopus 로고
    • Refined structure of orthorhombic lysozyme crystallized at high temperature: Correlation between morphology and intermolecular contacts
    • Oki, H., Matsuura, Y., Komatsu, H., and Chernov, A. A. 1999. Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology and intermolecular contacts. Acta Crystallographica D 55:114.
    • (1999) Acta Crystallographica D , vol.55 , pp. 114
    • Oki, H.1    Matsuura, Y.2    Komatsu, H.3    Chernov, A.A.4
  • 38
    • 0028268603 scopus 로고
    • Synthetic, structural and biological studies of the ubiquitin system: The total chemical synthesis of ubiquitin
    • Ramage, R., Green, J., Muir, T. W., Ogunjobi, O. M., Love, S., and Shaw, K. 1994. Synthetic, structural and biological studies of the ubiquitin system: the total chemical synthesis of ubiquitin. Journal of Biochemistry 299:151-158.
    • (1994) Journal of Biochemistry , vol.299 , pp. 151-158
    • Ramage, R.1    Green, J.2    Muir, T.W.3    Ogunjobi, O.M.4    Love, S.5    Shaw, K.6
  • 39
    • 0037139549 scopus 로고    scopus 로고
    • De novo determination of protein backbone structure from residual dipolar couplings using Rosetta
    • Rohl, C. A., and Baker, D. 2002. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemistry Society 124:2723-2729.
    • (2002) Journal of the American Chemistry Society , vol.124 , pp. 2723-2729
    • Rohl, C.A.1    Baker, D.2
  • 40
    • 0002660809 scopus 로고
    • The detection of sub-units within the crystallographic asymmetric unit
    • Rossman, M. G., and Blow, D. M. 1962. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallographica 15:24-31.
    • (1962) Acta Crystallographica , vol.15 , pp. 24-31
    • Rossman, M.G.1    Blow, D.M.2
  • 41
    • 85069111741 scopus 로고
    • Excision and applications
    • chapter 6. Springer-Verlag, Berlin
    • Rotman, J. J. 1988. Excision and applications. An Introduction to Algebraic Topology, chapter 6. Springer-Verlag, Berlin, p. 123.
    • (1988) An Introduction to Algebraic Topology , pp. 123
    • Rotman, J.J.1
  • 42
    • 85069117140 scopus 로고
    • Quaternions
    • Massachusetts Institute of Technology, AI Laboratory, M. Beeler et al., editors, February 29. Item 107
    • Salamin, E. 1972. Quaternions. HAKMEM. Artificial Intelligence Memo No. 239, Massachusetts Institute of Technology, AI Laboratory, M. Beeler et al., editors, February 29. Item 107. http://www.inwap.com/pdp10/hbaker/hakmem/hakmem. html.
    • (1972) HAKMEM. Artificial Intelligence Memo No. 239 , vol.239
    • Salamin, E.1
  • 43
    • 24744432063 scopus 로고
    • Applications of quaternions to computation with rotations
    • Stanford University, AI Laboratory
    • Salamin, E. 1979. Applications of quaternions to computation with rotations. Internal working paper, Stanford University, AI Laboratory.
    • (1979) Internal Working Paper
    • Salamin, E.1
  • 44
    • 84967789667 scopus 로고
    • Recent results in the field of liquid crystals
    • Saupe, A. 1968. Recent results in the field of liquid crystals. Angewandte Chemie 7:97-112.
    • (1968) Angewandte Chemie , vol.7 , pp. 97-112
    • Saupe, A.1
  • 46
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high affinity ligands for proteins: SAR by NMR
    • Shuker, S. B., Hajduk, P. J., Meadows, R. P., and Fesik, S. W. 1996. Discovering high affinity ligands for proteins: SAR by NMR. Science 274:1531-1534.
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 47
    • 0035965759 scopus 로고    scopus 로고
    • A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones
    • Tian, F., Valafar, H., and Prestegard, J. H. 2001. A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. Journal of the American Chemistry Society 123:11,791-11,796.
    • (2001) Journal of the American Chemistry Society , vol.123 , pp. 11
    • Tian, F.1    Valafar, H.2    Prestegard, J.H.3
  • 48
    • 0030722243 scopus 로고    scopus 로고
    • Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
    • Tjandra, N., and Bax, A. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111-1114.
    • (1997) Science , vol.278 , pp. 1111-1114
    • Tjandra, N.1    Bax, A.2
  • 49
    • 0000695363 scopus 로고    scopus 로고
    • High-resolution structure (1.33 angstrom) of aHEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission
    • Vaney, M. C., Maignan, S., Ries-Kautt, M., and Ducruix, A. 1996. High-resolution structure (1.33 angstrom) of aHEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystallographica D 52:505-517.
    • (1996) Acta Crystallographica D , vol.52 , pp. 505-517
    • Vaney, M.C.1    Maignan, S.2    Ries-Kautt, M.3    Ducruix, A.4
  • 51
    • 3042719896 scopus 로고    scopus 로고
    • Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure
    • Wang, L., and Donald, B. R. 2004. Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. Journal of Biomolecular NMR 29(3):223-242.
    • (2004) Journal of Biomolecular NMR , vol.29 , Issue.3 , pp. 223-242
    • Wang, L.1    Donald, B.R.2
  • 52
    • 0036180645 scopus 로고    scopus 로고
    • Exact solutions for chemical bond orientations from residual dipolar couplings
    • Wedemeyer, W. J., Rohl, C. A., and Scheraga, H. A. 2002. Exact solutions for chemical bond orientations from residual dipolar couplings. Journal of Biomolecular NMR 22:137-151.
    • (2002) Journal of Biomolecular NMR , vol.22 , pp. 137-151
    • Wedemeyer, W.J.1    Rohl, C.A.2    Scheraga, H.A.3


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