메뉴 건너뛰기




Volumn 9781461451280, Issue , 2013, Pages 315-328

Distance geometry for realistic molecular conformations

Author keywords

[No Author keywords available]

Indexed keywords

ALGEBRA; COMPUTATIONAL CHEMISTRY; GEOMETRY; NUCLEAR MAGNETIC RESONANCE; PROTEINS;

EID: 84893859684     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-5128-0_15     Document Type: Chapter
Times cited : (2)

References (102)
  • 1
    • 0038825237 scopus 로고    scopus 로고
    • Stochastic proximity embedding
    • Agrafiotis, D.K.: Stochastic proximity embedding. J. Comput. Chem. 24(10), 1215-1221 (2003)
    • (2003) J. Comput. Chem. , vol.24 , Issue.10 , pp. 1215-1221
    • Agrafiotis, D.K.1
  • 2
    • 0030377824 scopus 로고    scopus 로고
    • Protein structure alignment using dynamic programming and iterative improvement
    • Akutsu, T.: Protein structure alignment using dynamic programming and iterative improvement. IEICE Trans. Inform. Syst. E79-D, 1-8 (1996)
    • (1996) IEICE Trans. Inform. Syst. E79-D , pp. 1-8
    • Akutsu, T.1
  • 3
    • 0002740666 scopus 로고    scopus 로고
    • Solving Euclidean distance matrix completion problems via semidefinite programming
    • Alfakih, A.Y., Khandani, A., Wolkowicz, H.: Solving Euclidean distance matrix completion problems via semidefinite programming. Comput. Optim. Appl. 12, 13-30 (1999)
    • (1999) Comput. Optim. Appl. , vol.12 , pp. 13-30
    • Alfakih, A.Y.1    Khandani, A.2    Wolkowicz, H.3
  • 4
    • 10844225367 scopus 로고    scopus 로고
    • Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
    • Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M.: Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58, 22-30 (2005)
    • (2005) Proteins , vol.58 , pp. 22-30
    • Bastolla, U.1    Porto, M.2    Roman, H.E.3    Vendruscolo, M.4
  • 5
    • 0029866846 scopus 로고    scopus 로고
    • Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water
    • Berndt, K.D., Guentert, P., Wuethrich, K.: Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water. Proteins 24, 304-313 (1996)
    • (1996) Proteins , vol.24 , pp. 304-313
    • Berndt, K.D.1    Guentert, P.2    Wuethrich, K.3
  • 6
    • 36449003225 scopus 로고
    • Molecular dynamics free energy calculation in four dimensions
    • Beutler, T.C., van Gunsteren, W.F.: Molecular dynamics free energy calculation in four dimensions. J. Chem. Phys. 101, 1417-1422 (1994)
    • (1994) J. Chem. Phys. , vol.101 , pp. 1417-1422
    • Beutler, T.C.1    Van Gunsteren, W.F.2
  • 8
    • 0029022355 scopus 로고
    • Conformational variability of solution NMR structures
    • Bonvin, A.M.J.J., Brünger, A.T.: Conformational variability of solution NMR structures. J. Mol. Biol. 250, 80-93 (1995)
    • (1995) J. Mol. Biol. , vol.250 , pp. 80-93
    • Bonvin, A.M.J.J.1    Brünger, A.T.2
  • 9
    • 0027474781 scopus 로고
    • "Ensemble" iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin
    • Bonvin, A.M.J.J., Rullmann, J.A.C., Lamerichs, R.M.J.N., Boelens, R., Kaptein, R.: "Ensemble" iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin. Proteins Struct. Funct. Genet. 15, 385-400 (1993)
    • (1993) Proteins Struct. Funct. Genet. , vol.15 , pp. 385-400
    • Bonvin, A.M.J.J.1    Rullmann, J.A.C.2    Lamerichs, R.M.J.N.3    Boelens, R.4    Kaptein, R.5
  • 10
    • 85193186859 scopus 로고
    • Distance geometry in distance and torsion angle space: Flexibility, convergence and sampling properties
    • Renugoplakrishnan, V. (ed.) ESCOM, Leiden, Netherlands
    • Braun, W.: Distance geometry in distance and torsion angle space: Flexibility, convergence and sampling properties. In: Renugoplakrishnan, V. (ed.) Proteins, pp. 116-22. ESCOM, Leiden, Netherlands (1991)
    • (1991) Proteins, Pp. , pp. 116-122
    • Braun, W.1
  • 11
    • 52049122134 scopus 로고    scopus 로고
    • Extending the geometric build-up algorithm for the molecular distance geometry problem
    • Carvalho, R., Lavor, C., Protti, F.: Extending the geometric build-up algorithm for the molecular distance geometry problem. Inform. Process. Lett. 108(4), 234-237 (2008)
    • (2008) Inform. Process. Lett. , vol.108 , Issue.4 , pp. 234-237
    • Carvalho, R.1    Lavor, C.2    Protti, F.3
  • 12
    • 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., Bax, A.: A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J. Mag. Reson. 133, 216-221 (1998)
    • (1998) J. Mag. Reson. , vol.133 , pp. 216-221
    • Clore, G.M.1    Gronenborn, A.M.2    Bax, A.3
  • 13
    • 0032012610 scopus 로고    scopus 로고
    • Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
    • Clore, G.M., Gronenborn, A.M., Tjandra, N.: Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Mag. Reson. 131, 159-162 (1998)
    • (1998) J. Mag. Reson. , vol.131 , pp. 159-162
    • Clore, G.M.1    Gronenborn, A.M.2    Tjandra, N.3
  • 14
    • 0013392188 scopus 로고
    • Conformational sampling by a general linearized embedding algorithm
    • Crippen, G.M., Smellie, A.S., Richardson, W.W.: Conformational sampling by a general linearized embedding algorithm. J. Comput. Chem. 13(10), 1262-1274 (1992)
    • (1992) J. Comput. Chem. , vol.13 , Issue.10 , pp. 1262-1274
    • Crippen, G.M.1    Smellie, A.S.2    Richardson, W.W.3
  • 15
    • 0011962258 scopus 로고
    • Chemical distance geometry: Current realization and future projection
    • Crippen, G.M.: Chemical distance geometry: Current realization and future projection. J. Math. Chem. 6, 307-324 (1991)
    • (1991) J. Math. Chem. , vol.6 , pp. 307-324
    • Crippen, G.M.1
  • 16
    • 3042693653 scopus 로고    scopus 로고
    • Cluster distance geometry of polypeptide chains
    • Crippen, G.M.: Cluster distance geometry of polypeptide chains. J. Comput. Chem. 25, 1305-1312 (2004)
    • (2004) J. Comput. Chem. , vol.25 , pp. 1305-1312
    • Crippen, G.M.1
  • 17
    • 84986450030 scopus 로고
    • Exploring the conformation space of cycloalkanes by linearized embedding
    • Crippen, G.M.: Exploring the conformation space of cycloalkanes by linearized embedding. J. Comput. Chem. 13(3), 351-361 (1992)
    • (1992) J. Comput. Chem. , vol.13 , Issue.3 , pp. 351-361
    • Crippen, G.M.1
  • 18
    • 19544366594 scopus 로고    scopus 로고
    • Recognizing protein folds by cluster distance geometry
    • Crippen, G.M.: Recognizing protein folds by cluster distance geometry. Proteins 60, 82-89 (2005)
    • (2005) Proteins , vol.60 , pp. 82-89
    • Crippen, G.M.1
  • 19
    • 7044240651 scopus 로고    scopus 로고
    • Statistical mechanics of protein folding by cluster distance geometry
    • Crippen, G.M.: Statistical mechanics of protein folding by cluster distance geometry. Biopolymers 75(3), 278-289 (2004)
    • (2004) Biopolymers , vol.75 , Issue.3 , pp. 278-289
    • Crippen, G.M.1
  • 21
    • 0025472891 scopus 로고
    • Global energy minimization by rotational energy embedding
    • Crippen, G.M., Havel, T.F.: Global energy minimization by rotational energy embedding. J. Chem. Inform. Comput. Sci. 30(3), 222-7 (1990)
    • (1990) J. Chem. Inform. Comput. Sci. , vol.30 , Issue.3 , pp. 222-227
    • Crippen, G.M.1    Havel, T.F.2
  • 22
    • 0030840021 scopus 로고    scopus 로고
    • Accounting for conformational variability in NMR structure of cyclopeptides: Ensemble averaging of interproton distance and coupling constant restraints
    • Cuniasse, P., Raynal, I., Yiotakis, A., Dive, V.: Accounting for conformational variability in NMR structure of cyclopeptides: Ensemble averaging of interproton distance and coupling constant restraints. J. Am. Chem. Soc. 119, 5239-5248 (1997)
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5239-5248
    • Cuniasse, P.1    Raynal, I.2    Yiotakis, A.3    Dive, V.4
  • 23
    • 21844516195 scopus 로고
    • Straightening Euclidean invariants
    • Dalbec, J.P.: Straightening Euclidean invariants. Ann. Math. Artif. Intell. 13, 97-108 (1995)
    • (1995) Ann. Math. Artif. Intell. , vol.13 , pp. 97-108
    • Dalbec, J.P.1
  • 24
  • 25
    • 33750957169 scopus 로고    scopus 로고
    • New general tools for constrained geometry optimizations
    • De Vico, L., Olivucci, M., Lindh, R.: New general tools for constrained geometry optimizations. J. Chem. Theor. Comput. 1, 1029-1037 (2005)
    • (2005) J. Chem. Theor. Comput. , vol.1 , pp. 1029-1037
    • De Vico, L.1    Olivucci, M.2    Lindh, R.3
  • 26
    • 31244436296 scopus 로고    scopus 로고
    • A Linear-time algorithm for solving the molecular distance geometry problem with exact interatomic distances
    • Dong, Q., Wu, Z.: A Linear-time algorithm for solving the molecular distance geometry problem with exact interatomic distances. J. Global Optim. 22, 365-375 (2002)
    • (2002) J. Global Optim. , vol.22 , pp. 365-375
    • Dong, Q.1    Wu, Z.2
  • 27
    • 84867962761 scopus 로고    scopus 로고
    • A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data
    • Dong, Q., Wu, Z.: A geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data. J. Global Optim. 26(3), 321-333 (2003)
    • (2003) J. Global Optim. , vol.26 , Issue.3 , pp. 321-333
    • Dong, Q.1    Wu, Z.2
  • 28
    • 0343402093 scopus 로고
    • Distance geometry and geometric algebra
    • Dress, A.W.M., Havel, T.F.: Distance geometry and geometric algebra. Found. Phys. 23, 1357-1374 (1993)
    • (1993) Found. Phys. , vol.23 , pp. 1357-1374
    • Dress, A.W.M.1    Havel, T.F.2
  • 29
    • 34250085320 scopus 로고
    • Classifying the conformations of a chemical system using matrices of integers
    • Easthope, P.L.: Classifying the conformations of a chemical system using matrices of integers. J. Math. Chem. 13, 73-94 (1993)
    • (1993) J. Math. Chem. , vol.13 , pp. 73-94
    • Easthope, P.L.1
  • 30
    • 17744384497 scopus 로고    scopus 로고
    • Molecular conformation search by distance matrix perturbations
    • Emiris, I.Z., Nikitopoulos, T.G.: Molecular conformation search by distance matrix perturbations. J. Math. Chem. 37(3), 233-253 (2005)
    • (2005) J. Math. Chem. , vol.37 , Issue.3 , pp. 233-253
    • Emiris, I.Z.1    Nikitopoulos, T.G.2
  • 31
    • 0035324941 scopus 로고    scopus 로고
    • Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations
    • Feuston, B.P., Miller, M.D., Culberson, J.C., Nachbar, R.B., Kearsley, S.K.: Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations. J. Chem. Inform. Comput. Sci. 41(3), 754-763 (2001)
    • (2001) J. Chem. Inform. Comput. Sci. , vol.41 , Issue.3 , pp. 754-763
    • Feuston, B.P.1    Miller, M.D.2    Culberson, J.C.3    Nachbar, R.B.4    Kearsley, S.K.5
  • 32
    • 0033030023 scopus 로고    scopus 로고
    • Application of distance geometry to 3D visualization of sequence relationships
    • Forster, M.J., Heath, A.B., Afzal, M.A.: Application of distance geometry to 3D visualization of sequence relationships. Bioinformatics 15(1), 89-90 (1999)
    • (1999) Bioinformatics , vol.15 , Issue.1 , pp. 89-90
    • Forster, M.J.1    Heath, A.B.2    Afzal, M.A.3
  • 33
    • 0025310080 scopus 로고
    • Computational Methods for Determining Protein Structures from NMR Data
    • Gippert, G.P., Yip, P.F., Wright, P.E., Case, D.A.: Computational Methods for Determining Protein Structures from NMR Data. Biochem. Pharmacol. 40, 15-22 (1990)
    • (1990) Biochem. Pharmacol. , vol.40 , pp. 15-22
    • Gippert, G.P.1    Yip, P.F.2    Wright, P.E.3    Case, D.A.4
  • 34
    • 0034744532 scopus 로고    scopus 로고
    • Improved convergence and speed for the distance geometry program APA to determine protein structure
    • Glunt, W., Hayden, T.: Improved convergence and speed for the distance geometry program APA to determine protein structure. Comput. Chem. 25, 223-230 (2001)
    • (2001) Comput. Chem. , vol.25 , pp. 223-230
    • Glunt, W.1    Hayden, T.2
  • 35
    • 0000771519 scopus 로고
    • An Alternating Projection Algorithm for Computing the Nearest Euclidean Distance Matrix
    • Glunt, W., Hayden, T.L., Hong, S., Wells, J.: An Alternating Projection Algorithm for Computing the Nearest Euclidean Distance Matrix. SIAM J. Matrix Anal. Appl. 11, 589-600 (1990)
    • (1990) SIAM J. Matrix Anal. Appl. , vol.11 , pp. 589-600
    • Glunt, W.1    Hayden, T.L.2    Hong, S.3    Wells, J.4
  • 36
    • 0025986584 scopus 로고
    • The Embedding Problem for Predistance Matrices
    • Glunt, W., Hayden, T.L., Liu, W.M.: The Embedding Problem for Predistance Matrices. Bull. Math. Biol. 53, 769-796 (1991)
    • (1991) Bull. Math. Biol. , vol.53 , pp. 769-796
    • Glunt, W.1    Hayden, T.L.2    Liu, W.M.3
  • 37
    • 0000922470 scopus 로고
    • Molecular conformations from distance matrixes
    • Glunt, W., Hayden, T.L., Raydan, M.: Molecular conformations from distance matrixes. J. Comput. Chem. 14(1), 114-120 (1993)
    • (1993) J. Comput. Chem. , vol.14 , Issue.1 , pp. 114-120
    • Glunt, W.1    Hayden, T.L.2    Raydan, M.3
  • 38
    • 84986533367 scopus 로고
    • Preconditioners for distance matrix algorithms
    • Glunt, W., Hayden, T.L., Raydan, M.: Preconditioners for distance matrix algorithms. J. Comput. Chem. 15, 227-232 (1994)
    • (1994) J. Comput. Chem. , vol.15 , pp. 227-232
    • Glunt, W.1    Hayden, T.L.2    Raydan, M.3
  • 39
    • 68149166355 scopus 로고    scopus 로고
    • Molecular embedding via a second order dissimilarity parameterized approach
    • Grooms, I.G., Lewis, R.M., Trosset, M.W.: Molecular embedding via a second order dissimilarity parameterized approach. SIAM J. Sci. Comput. 31, 2733-2756 (2009)
    • (2009) SIAM J. Sci. Comput. , vol.31 , pp. 2733-2756
    • Grooms, I.G.1    Lewis, R.M.2    Trosset, M.W.3
  • 40
    • 67449096625 scopus 로고    scopus 로고
    • Solving molecular distance geometry problems by global optimization algorithms
    • Grosso, A., Locatelli, M., Schoen, F.: Solving molecular distance geometry problems by global optimization algorithms. Comput. Optim. Appl. 43(1), 23-37 (2009)
    • (2009) Comput. Optim. Appl. , vol.43 , Issue.1 , pp. 23-37
    • Grosso, A.1    Locatelli, M.2    Schoen, F.3
  • 41
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculations with the new program DYANA
    • Guentert, P., Mumenthaler, C., Wuethrich, K.: Torsion angle dynamics for NMR structure calculations with the new program DYANA. J. Mol. Biol. 273, 283-298 (1997)
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Guentert, P.1    Mumenthaler, C.2    Wuethrich, K.3
  • 42
    • 0026078528 scopus 로고
    • Explicit distance geometry: Identification of all the degrees of freedom in a large RNA molecule
    • Hadwiger, M.A., Fox, G.E.: Explicit distance geometry: Identification of all the degrees of freedom in a large RNA molecule. J. Biomol. Struct.Dynam. 8(4), 759-779 (1991)
    • (1991) J. Biomol. Struct.Dynam. , vol.8 , Issue.4 , pp. 759-779
    • Hadwiger, M.A.1    Fox, G.E.2
  • 43
  • 44
    • 0025932859 scopus 로고
    • An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance
    • Havel, T.F.: An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Progress Biophys. Mol. Biol. 56, 43-78 (1991)
    • (1991) Progress Biophys. Mol. Biol. , vol.56 , pp. 43-78
    • Havel, T.F.1
  • 45
    • 0013433957 scopus 로고    scopus 로고
    • Distance geometry: Theory, algorithms, and chemical applications
    • von Rague, P., Schreiner, P.R., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer, H.F. (eds.) Wiley, New York
    • Havel, T.F.: Distance geometry: Theory, algorithms, and chemical applications, In: von Rague, P., Schreiner, P.R., Allinger, N.L., Clark, T., Gasteiger, J., Kollman, P.A., Schaefer, H.F. (eds.) Encyclopedia of Computational Chemistry, pp. 723-742. Wiley, New York (1998)
    • (1998) Encyclopedia of Computational Chemistry , pp. 723-742
    • Havel, T.F.1
  • 46
    • 33847302188 scopus 로고    scopus 로고
    • Distance Geometry
    • Grant, D.M., Harris, R.K. (eds.) Wiley, New York
    • Havel, T.F.: Distance Geometry. In: Grant, D.M., Harris, R.K. (eds.) Invited contribution to the Encyclopedia of NMR, pp. 1701-1710. Wiley, New York (1996)
    • (1996) Invited Contribution to the Encyclopedia of NMR, Pp. , pp. 1701-1710
    • Havel, T.F.1
  • 47
    • 0242351022 scopus 로고    scopus 로고
    • Metric matrix embedding in protein structure calculations, NMR spectra analysis, and relaxation theory
    • Havel, T.F.: Metric matrix embedding in protein structure calculations, NMR spectra analysis, and relaxation theory. Mag. Reson. Chem. 41, 537-550 (2003)
    • (2003) Mag. Reson. Chem. , vol.41 , pp. 537-550
    • Havel, T.F.1
  • 48
    • 0025294066 scopus 로고
    • The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations
    • Havel, T.F.: The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: a study of 1830 independently computed conformations. Biopolymers 29(12-13), 1565-1585 (1990)
    • (1990) Biopolymers , vol.29 , Issue.12-13 , pp. 1565-1585
    • Havel, T.F.1
  • 51
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L., Sander, C.: Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993)
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 52
    • 0031687654 scopus 로고    scopus 로고
    • Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures
    • Huang, E.S., Samudrala, R., Ponder, J.W.: Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Sci. 7, 1998-2003 (1998)
    • (1998) Protein Sci. , vol.7 , pp. 1998-2003
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 53
    • 0031211551 scopus 로고    scopus 로고
    • Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics
    • Huber, T., Torda, A.E., van Gunsteren, W.F.: Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics. J. Phys. Chem. A101, 5926-5930 (1997)
    • (1997) J. Phys. Chem. A , vol.101 , pp. 5926-5930
    • Huber, T.1    Torda, A.E.2    Van Gunsteren, W.F.3
  • 54
    • 85193170738 scopus 로고
    • Determination of three-dimensional structures of proteins in solution by NMR experiment and distance geometry calculation
    • Ikura, T., Go, N.: Determination of three-dimensional structures of proteins in solution by NMR experiment and distance geometry calculation. Kobunshi 39(3), 210-213 (1990)
    • (1990) Kobunshi , vol.39 , Issue.3 , pp. 210-213
    • Ikura, T.1    Go, N.2
  • 56
    • 33646033429 scopus 로고    scopus 로고
    • Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model
    • Jacobs, D.J., Livesay, D.R., Hules, J., Tasayco, M.L.: Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. J. Mol. Biol. 358, 882-904 (2006)
    • (2006) J. Mol. Biol. , vol.358 , pp. 882-904
    • Jacobs, D.J.1    Livesay, D.R.2    Hules, J.3    Tasayco, M.L.4
  • 57
    • 0029334378 scopus 로고
    • Dynamic modelling of a helical peptide in solution using NMR data: Multiple conformations and multi-spin effects
    • Kemmink, J., Scheek, R.M.: Dynamic modelling of a helical peptide in solution using NMR data: Multiple conformations and multi-spin effects. J. Biomol. NMR 5, 33-40 (1995)
    • (1995) J. Biomol. NMR , vol.5 , pp. 33-40
    • Kemmink, J.1    Scheek, R.M.2
  • 58
    • 0026601051 scopus 로고
    • Computing the geometry of a molecule in dihedral angle space using NMR derived constraints. A new algorithm based on optimal filtering
    • Koehl, P., Lefevre, J.F., Jardetzky, O.: Computing the geometry of a molecule in dihedral angle space using NMR derived constraints. A new algorithm based on optimal filtering. J. Mol. Biol. 223(1), 299-315 (1992)
    • (1992) J. Mol. Biol. , vol.223 , Issue.1 , pp. 299-315
    • Koehl, P.1    Lefevre, J.F.2    Jardetzky, O.3
  • 59
    • 0043032425 scopus 로고    scopus 로고
    • Use of very long-distance NOEs in a fully deuterated protein: An approach for rapid protein fold determination
    • Koharudin, L.M.I., Bonvin, A.M.J.J., Kaptein, R., Boelens, R.: Use of very long-distance NOEs in a fully deuterated protein: An approach for rapid protein fold determination. J. Mag. Reson. 163, 228-225 (2003)
    • (2003) J. Mag. Reson. , vol.163 , pp. 228-225
    • Koharudin, L.M.I.1    Bonvin, A.M.J.J.2    Kaptein, R.3    Boelens, R.4
  • 60
    • 0026676167 scopus 로고
    • Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
    • Kuszewski, J., Nilges, M., Brunger, A.T.: Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm. J. Biomol. NMR 2, 33-56 (1992)
    • (1992) J. Biomol. NMR , vol.2 , pp. 33-56
    • Kuszewski, J.1    Nilges, M.2    Brunger, A.T.3
  • 61
    • 0036568284 scopus 로고    scopus 로고
    • Hamming distance geometry of a protein conformational space: Application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
    • Laboulais, C., Ouali, M., Bret, M.L., Gabarro-Arpa, J.: Hamming distance geometry of a protein conformational space: Application to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core. Protein. Struct. Funct. Genet. 47, 169-179 (2002)
    • (2002) Protein. Struct. Funct. Genet. , vol.47 , pp. 169-179
    • Laboulais, C.1    Ouali, M.2    Bret, M.L.3    Gabarro-Arpa, J.4
  • 62
    • 0010444309 scopus 로고
    • A combined model-building and distance geometry approach to automated conformational analysis and search
    • Leach, A.R., Smellie, A.S.: A combined model-building and distance geometry approach to automated conformational analysis and search. J. Chem. Inform. Comput. Sci. 32, 379-385 (1992)
    • (1992) J. Chem. Inform. Comput. Sci. , vol.32 , pp. 379-385
    • Leach, A.R.1    Smellie, A.S.2
  • 63
    • 59449085654 scopus 로고    scopus 로고
    • Double variable neighbourhood search with smoothing for the molecular distance geometry problem
    • Liberti, L., Lavor, C., Maculan, N., Marinelli, F.: Double variable neighbourhood search with smoothing for the molecular distance geometry problem. J. Global Optim. 43, 207-218 (2009)
    • (2009) J. Global Optim. , vol.43 , pp. 207-218
    • Liberti, L.1    Lavor, C.2    MacUlan, N.3    Marinelli, F.4
  • 64
    • 84863430641 scopus 로고    scopus 로고
    • Molecular distance geometry methods: From continuous to discrete
    • Liberti, L., Lavor, C., Mucherino, A., Maculan, N.: Molecular distance geometry methods: From continuous to discrete. Int. Trans. Oper. Res. 18(1), 33-51 (2011)
    • (2011) Int. Trans. Oper. Res. , vol.18 , Issue.1 , pp. 33-51
    • Liberti, L.1    Lavor, C.2    Mucherino, A.3    MacUlan, N.4
  • 65
    • 0026223897 scopus 로고
    • Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities
    • Mertz, J.E., Guentert, P., Wuethrich, K., Braun, W.: Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities. J. Biomol. NMR 1(3), 257-269 (1991)
    • (1991) J. Biomol. NMR , vol.1 , Issue.3 , pp. 257-269
    • Mertz, J.E.1    Guentert, P.2    Wuethrich, K.3    Braun, W.4
  • 66
    • 0029401590 scopus 로고
    • Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain
    • Morikawa, S., Ogata, K., Sekikawa, A., Sarai, A., Ishii, S., Nishimura, Y., Nakamura, H.: Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain. J. Biomol. NMR 6, 294-305 (1995)
    • (1995) J. Biomol. NMR , vol.6 , pp. 294-305
    • Morikawa, S.1    Ogata, K.2    Sekikawa, A.3    Sarai, A.4    Ishii, S.5    Nishimura, Y.6    Nakamura, H.7
  • 67
    • 0000960523 scopus 로고    scopus 로고
    • ε-optimal solutions to distance geometry problems via global continuation
    • Pardalos, P.M., Shalloway, D., Xue, G. (eds.) American Mathematical Society, Providence
    • Moré, J.J., Wu, Z.: ε-optimal solutions to distance geometry problems via global continuation. In: Pardalos, P.M., Shalloway, D., Xue, G. (eds.) Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, pp. 151-168. American Mathematical Society, Providence (1996)
    • (1996) Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Pp. , pp. 151-168
    • Moré, J.J.1    Wu, Z.2
  • 68
    • 0031285908 scopus 로고    scopus 로고
    • Global continuation for distance geometry problems
    • Moré, J.J., Wu, Z.: Global continuation for distance geometry problems. SIAM J. Optim. 7, 814-836 (1997)
    • (1997) SIAM J. Optim. , vol.7 , pp. 814-836
    • Moré, J.J.1    Wu, Z.2
  • 69
    • 0000935435 scopus 로고    scopus 로고
    • Distance geometry optimization for protein structures
    • Moré, J.J., Wu, Z.: Distance geometry optimization for protein structures. J. Global Optim. 15, 219-234 (1999)
    • (1999) J. Global Optim. , vol.15 , pp. 219-234
    • Moré, J.J.1    Wu, Z.2
  • 70
    • 0031486766 scopus 로고    scopus 로고
    • Embedding with a rigid substructure
    • Najfeld, I., Havel, T.F.: Embedding with a rigid substructure. J. Math. Chem. 21, 223-260 (1997)
    • (1997) J. Math. Chem. , vol.21 , pp. 223-260
    • Najfeld, I.1    Havel, T.F.2
  • 71
    • 0027347355 scopus 로고
    • Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties
    • Nakai, T., Kidera, A., Nakamura, H.: Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties. J. Biomol. NMR 3, 19-40 (1993)
    • (1993) J. Biomol. NMR , vol.3 , pp. 19-40
    • Nakai, T.1    Kidera, A.2    Nakamura, H.3
  • 72
    • 0004026778 scopus 로고
    • Sampling properties of simulated annealing and distance geometry
    • Nilges, M., Kuszewski, J., Brunger, A.T.: Sampling properties of simulated annealing and distance geometry. NATO ASI Series, Series A, 225, 451-455 (1991)
    • (1991) NATO ASI Series Series A , vol.225 , pp. 451-455
    • Nilges, M.1    Kuszewski, J.2    Brunger, A.T.3
  • 73
    • 0027463598 scopus 로고
    • Application of distance geometry to the proton assignment problem
    • Oshiro, C.M., Kuntz, I.D.: Application of distance geometry to the proton assignment problem. Biopolymers 33(1), 107-115 (1993)
    • (1993) Biopolymers , vol.33 , Issue.1 , pp. 107-115
    • Oshiro, C.M.1    Kuntz, I.D.2
  • 74
    • 0026203784 scopus 로고
    • Effects of limited input distance constraints upon the distance geometry algorithm
    • Oshiro, C.M., Thomason, J., Kuntz, I.D.: Effects of limited input distance constraints upon the distance geometry algorithm. Biopolymers 31(9), 1049-1064 (1991)
    • (1991) Biopolymers , vol.31 , Issue.9 , pp. 1049-1064
    • Oshiro, C.M.1    Thomason, J.2    Kuntz, I.D.3
  • 75
    • 0025909419 scopus 로고
    • Topological mirror images in protein structure computation: An underestimated problem
    • Pastore, A., Atkinson, R.A., Saudek, V., Williams, R.J.P.: Topological mirror images in protein structure computation: An underestimated problem. Protein. Struct. Funct. Genet. 10(1), 22-32 (1991)
    • (1991) Protein. Struct. Funct. Genet. , vol.10 , Issue.1 , pp. 22-32
    • Pastore, A.1    Atkinson, R.A.2    Saudek, V.3    Williams, R.J.P.4
  • 76
    • 0002485251 scopus 로고
    • How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches
    • Pearlman, D.A.: How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches. J. Biomol. NMR 4, 1-16 (1994)
    • (1994) J. Biomol. NMR , vol.4 , pp. 1-16
    • Pearlman, D.A.1
  • 77
    • 84986522804 scopus 로고
    • Improvements to the distance geometry algorithm for conforma-tional sampling of cyclic structures
    • Peishoff, C.E., Dixon, J.S.: Improvements to the distance geometry algorithm for conforma-tional sampling of cyclic structures. J. Comput. Chem. 13(5), 565-569 (1992)
    • (1992) J. Comput. Chem. , vol.13 , Issue.5 , pp. 565-569
    • Peishoff, C.E.1    Dixon, J.S.2
  • 78
    • 2442481958 scopus 로고    scopus 로고
    • Using redundant internal coordinates to optimize equilibrium geometries and transition states
    • Peng, C., Ayala, P.Y., Schlegel, H.B., Frisch, M.J.: Using redundant internal coordinates to optimize equilibrium geometries and transition states. J. Comput. Chem. 17, 49-56 (1996)
    • (1996) J. Comput. Chem. , vol.17 , pp. 49-56
    • Peng, C.1    Ayala, P.Y.2    Schlegel, H.B.3    Frisch, M.J.4
  • 79
    • 0002379892 scopus 로고
    • 3D molecular structures: Generation and use in 3D searching
    • Kubinyi, H. (ed.) ESCOM Science Publishers, Leiden, The Netherlands
    • Perlman, R.S.: 3D molecular structures: Generation and use in 3D searching. In: Kubinyi, H. (ed.) 3D-QSAR in Drug Design: Theory, Methods and Applications. ESCOM Science Publishers, Leiden, The Netherlands (1993)
    • (1993) 3D-QSAR in Drug Design: Theory, Methods and Applications
    • Perlman, R.S.1
  • 80
    • 0037474530 scopus 로고    scopus 로고
    • Modelling zinc-binding proteins with GADGET: Genetic algorithm and distance geometry for exploring topology
    • Petersen, K., Taylor, W.R.: Modelling zinc-binding proteins with GADGET: Genetic algorithm and distance geometry for exploring topology. J. Mol. Biol. 325(5), 1039-1059 (2003)
    • (2003) J. Mol. Biol. , vol.325 , Issue.5 , pp. 1039-1059
    • Petersen, K.1    Taylor, W.R.2
  • 81
    • 0038922502 scopus 로고
    • Circles, vectors, and linear algebra
    • Pfeifer, R.E., van Hook, C.: Circles, vectors, and linear algebra. Math. Mag. 66, 86 (1993)
    • (1993) Math. Mag. , vol.66 , pp. 86
    • Pfeifer, R.E.1    Van Hook, C.2
  • 83
    • 0034480326 scopus 로고    scopus 로고
    • NMR structures of biomolecules using field oriented media and residual dipolar couplings
    • Prestegard, J.H., Al-Hashimi, H.M., Tolman, J.R.: NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys. 33, 371-424 (2000)
    • (2000) Q. Rev. Biophys. , vol.33 , pp. 371-424
    • Prestegard, J.H.1    Al-Hashimi, H.M.2    Tolman, J.R.3
  • 84
    • 0034704222 scopus 로고    scopus 로고
    • Nonlinear dimensionality reduction by locally linear embedding
    • Rowels, S.T., Saul, L.K.: Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323-2326 (2000)
    • (2000) Science , vol.290 , pp. 2323-2326
    • Rowels, S.T.1    Saul, L.K.2
  • 85
    • 0027349406 scopus 로고
    • Derivation of locally accurate spatial protein structure from NMR data
    • Sherman, S.A., Johnson, M.E.: Derivation of locally accurate spatial protein structure from NMR data. Progress Biophys. Mol. Biol. 59, 285-339 (1993)
    • (1993) Progress Biophys. Mol. Biol. , vol.59 , pp. 285-339
    • Sherman, S.A.1    Johnson, M.E.2
  • 86
    • 47749090558 scopus 로고    scopus 로고
    • A remark on global positioning from local distances
    • Singer, A.: A remark on global positioning from local distances. Proc. Nat. Acad. Sci. 105, 9507-9511 (2008)
    • (2008) Proc. Nat. Acad. Sci. , vol.105 , pp. 9507-9511
    • Singer, A.1
  • 87
    • 70350370784 scopus 로고    scopus 로고
    • A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation
    • Sit, A., Wu, Z., Yuan, Y.: A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation. Bull. Math. Biol. 71(8), 1914-1933 (2009)
    • (2009) Bull. Math. Biol. , vol.71 , Issue.8 , pp. 1914-1933
    • Sit, A.1    Wu, Z.2    Yuan, Y.3
  • 88
    • 0025783881 scopus 로고
    • Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function
    • Snow, M.E., Crippen, G.M.: Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function. Int. J. Peptide Protein Res. 38(2), 161-168 (1991)
    • (1991) Int. J. Peptide Protein Res. , vol.38 , Issue.2 , pp. 161-168
    • Snow, M.E.1    Crippen, G.M.2
  • 90
    • 0027510701 scopus 로고
    • An automated method for modeling proteins on known templates using distance geometry
    • Srinivasan, S., March, C.J., Sudarasanam, S.: An automated method for modeling proteins on known templates using distance geometry. Protein Sci. 2, 227-289 (1993)
    • (1993) Protein Sci. , vol.2 , pp. 227-289
    • Srinivasan, S.1    March, C.J.2    Sudarasanam, S.3
  • 91
    • 0034704229 scopus 로고    scopus 로고
    • A global geometric framework for nonlinear dimensionality reduction
    • Tenenbaum, J.B., de Silva, V., Langford, J.C.: A global geometric framework for nonlinear dimensionality reduction. Science 290, 2319-2322 (2000)
    • (2000) Science , vol.290 , pp. 2319-2322
    • Tenenbaum, J.B.1    De Silva, V.2    Langford, J.C.3
  • 92
    • 0025367860 scopus 로고
    • Time-averaged nuclear overhauser effect distance restraints applied to tendamistat
    • Torda, A.E., Scheek, R.M., van Gunsteren, W.F.: Time-averaged nuclear overhauser effect distance restraints applied to tendamistat. J. Mol. Biol. 214, 223-235 (1990)
    • (1990) J. Mol. Biol. , vol.214 , pp. 223-235
    • Torda, A.E.1    Scheek, R.M.2    Van Gunsteren, W.F.3
  • 94
    • 0027141511 scopus 로고
    • A structure refinement method based on molecular dynamics in four spatial dimensions
    • van Schaik, R.C., Berendsen, H.J.C., Torda, A.E., van Gunsteren, W.F.: A structure refinement method based on molecular dynamics in four spatial dimensions. J. Mol. Biol. 234, 751-762 (1993)
    • (1993) J. Mol. Biol. , vol.234 , pp. 751-762
    • Van Schaik, R.C.1    Berendsen, H.J.C.2    Torda, A.E.3    Van Gunsteren, W.F.4
  • 95
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • Vendruscolo, M., Kussell, E., Domany, E.: Recovery of protein structure from contact maps. Folding Des. 2, 295-306 (1997)
    • (1997) Folding Des. , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Kussell, E.2    Domany, E.3
  • 96
    • 33846263054 scopus 로고    scopus 로고
    • A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data
    • Wang, L., Mettu, R.R., Donald, B.R.: A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. J. Comput. Biol. 13(7), 1267-1288 (2006)
    • (2006) J. Comput. Biol. , vol.13 , Issue.7 , pp. 1267-1288
    • Wang, L.1    Mettu, R.R.2    Donald, B.R.3
  • 97
    • 0000121535 scopus 로고
    • Searching conformational space with the spectral distance geometry algorithm
    • Wells, C., Glunt, W., Hayden, T.L.: Searching conformational space with the spectral distance geometry algorithm. J. Mol. Struct. (Theochem) 308, 263-271 (1994)
    • (1994) J. Mol. Struct. (Theochem) , vol.308 , pp. 263-271
    • Wells, C.1    Glunt, W.2    Hayden, T.L.3
  • 98
    • 84986517060 scopus 로고
    • A comparison of distance geometry and molecular dynamics simulation techniques for conformational analysis of β-cyclodextrin
    • Wertz, D.A., Shi, C.X., Venanzi, C.A.: A comparison of distance geometry and molecular dynamics simulation techniques for conformational analysis of β-cyclodextrin. J. Comput. Chem. 13(1), 41-56 (1992)
    • (1992) J. Comput. Chem. , vol.13 , Issue.1 , pp. 41-56
    • Wertz, D.A.1    Shi, C.X.2    Venanzi, C.A.3
  • 99
    • 0035156982 scopus 로고    scopus 로고
    • Constrained global optimization for estimating molecular structure from atomic distances
    • Williams, G.A., Dugan, J.M., Altman, R.B.: Constrained global optimization for estimating molecular structure from atomic distances. J. Comput. Biol. 8(5), 523-547 (2001)
    • (2001) J. Comput. Biol. , vol.8 , Issue.5 , pp. 523-547
    • Williams, G.A.1    Dugan, J.M.2    Altman, R.B.3
  • 100
    • 33847251002 scopus 로고    scopus 로고
    • An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
    • Wu, D., Wu, Z.: An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data. J. Global Optim. 37, 661-673 (2007)
    • (2007) J. Global Optim. , vol.37 , pp. 661-673
    • Wu, D.1    Wu, Z.2
  • 102
    • 33750706214 scopus 로고    scopus 로고
    • Solving spatial constraints with global distance coordinate system
    • Yang, L.: Solving spatial constraints with global distance coordinate system. Int. J. Comput. Geom. Appl. 16, 533-547 (2006)
    • (2006) Int. J. Comput. Geom. Appl. , vol.16 , pp. 533-547
    • Yang, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.