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Volumn 285, Issue 4, 1999, Pages 1691-1710

A branch and bound algorithm for protein structure refinement from sparse NMR data sets

Author keywords

Annealing; Distance restraints; Global optimization; Protein folding

Indexed keywords

CARBON 13; NITROGEN 15;

EID: 0033613919     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2372     Document Type: Article
Times cited : (31)

References (41)
  • 2
    • 0003086747 scopus 로고    scopus 로고
    • Rigorous convex underestimators for general twice differentiable problems
    • Adjiman C. S., Floudas C. A. Rigorous convex underestimators for general twice differentiable problems. J. Global Optimization. 9:1996;23-40.
    • (1996) J. Global Optimization , vol.9 , pp. 23-40
    • Adjiman, C.S.1    Floudas, C.A.2
  • 3
    • 0032552250 scopus 로고    scopus 로고
    • A global optimization method, αbB, for general twice differentiable NLPs: I. Theoretical advances
    • Adjiman C. S., Dallwig S., Floudas C. A., Neumaier A. A global optimization method, αBB, for general twice differentiable NLPs: I. Theoretical advances. Comput. Chem. Eng. 22:1998a;1137-1158.
    • (1998) Comput. Chem. Eng. , vol.22 , pp. 1137-1158
    • Adjiman, C.S.1    Dallwig, S.2    Floudas, C.A.3    Neumaier, A.4
  • 4
    • 0032552252 scopus 로고    scopus 로고
    • A global optimization method, αbB, for general twice differentiable NLPs: II. Implementation and Computational Results
    • Adjiman C. S., Androulakis I. P., Floudas C. A. A global optimization method, αBB, for general twice differentiable NLPs: II. Implementation and Computational Results. Comput. Chem. Eng. 22:1998b;1159-1179.
    • (1998) Comput. Chem. Eng. , vol.22 , pp. 1159-1179
    • Adjiman, C.S.1    Androulakis, I.P.2    Floudas, C.A.3
  • 6
    • 0001327501 scopus 로고
    • αbB: A global optimization method for general constrained nonconvex problems
    • Androulakis I. P., Maranas C. D., Floudas C. A. αBB: a global optimization method for general constrained nonconvex problems. J. Global Opt. 7:1995;337-363.
    • (1995) J. Global Opt. , vol.7 , pp. 337-363
    • Androulakis, I.P.1    Maranas, C.D.2    Floudas, C.A.3
  • 7
    • 12044252858 scopus 로고
    • Methodological advances in protein NMR
    • Bax A., Grzesiek S. Methodological advances in protein NMR. Acc. Chem. Res. 26:1993;131-138.
    • (1993) Acc. Chem. Res. , vol.26 , pp. 131-138
    • Bax, A.1    Grzesiek, S.2
  • 9
    • 0022336792 scopus 로고
    • Calculation of protein conformations by protein-proton distance constraints, a new efficient algorithm
    • Braun W., Gō N. Calculation of protein conformations by protein-proton distance constraints, a new efficient algorithm. J. Mol. Biol. 186:1985;611-626.
    • (1985) J. Mol. Biol. , vol.186 , pp. 611-626
    • Braun, W.1    Go, N.2
  • 12
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential hydrophobic potential derived from X-ray structures of globular proteins is able to indentify native folds
    • Casari G., Sippl M. Structure-derived hydrophobic potential hydrophobic potential derived from X-ray structures of globular proteins is able to indentify native folds. J. Mol. Biol. 224:1992;725-732.
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.2
  • 13
    • 0025871254 scopus 로고
    • Structures of larger proteins in solution: Three- And four-dimensional heteronuclear NMR spectroscopy
    • Clore G. M., Gronenborn A. M. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy. Science. 252:1991;1390-1399.
    • (1991) Science , vol.252 , pp. 1390-1399
    • Clore, G.M.1    Gronenborn, A.M.2
  • 14
    • 0027965072 scopus 로고
    • X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates
    • Fedorov A. A., Magnus K. A., Graupe M. H., Lattman E. E., Pollard T. D., Almo S. C. X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates. Proc. Natl Acad. Sci. USA. 91:1994;8636-8640.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 8636-8640
    • Fedorov, A.A.1    Magnus, K.A.2    Graupe, M.H.3    Lattman, E.E.4    Pollard, T.D.5    Almo, S.C.6
  • 15
    • 0031027910 scopus 로고    scopus 로고
    • Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR
    • Gardener K. H., Rosen M. K., Kay L. E. Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. Biochemistry. 36:1997;1389-1401.
    • (1997) Biochemistry , vol.36 , pp. 1389-1401
    • Gardener, K.H.1    Rosen, M.K.2    Kay, L.E.3
  • 17
    • 0000335209 scopus 로고
    • Hierarchical algorithm for computer modeling of protein tertiary structure: Folding of myoglobin to 6.2 Å resolution
    • Gunn J., Monge A., Friesner R., Marshall C. Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 Å resolution. J. Phys. Chem. 98:1994;702-711.
    • (1994) J. Phys. Chem. , vol.98 , pp. 702-711
    • Gunn, J.1    Monge, A.2    Friesner, R.3    Marshall, C.4
  • 19
    • 0029871791 scopus 로고    scopus 로고
    • Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations
    • Huang E. S., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J. Mol. Biol. 257:1996;716-725.
    • (1996) J. Mol. Biol. , vol.257 , pp. 716-725
    • Huang, E.S.1    Subbiah, S.2    Tsai, J.3    Levitt, M.4
  • 20
    • 0141775243 scopus 로고
    • A hierarchical algorithm for polymer simulations
    • Johnson L., Monge A., Friesner R. A. A hierarchical algorithm for polymer simulations. J. Chem. Phys. 97:1992;9355-9365.
    • (1992) J. Chem. Phys. , vol.97 , pp. 9355-9365
    • Johnson, L.1    Monge, A.2    Friesner, R.A.3
  • 21
    • 84986532547 scopus 로고
    • Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water
    • Kitchen D. B., Hirata F., Westbrook J. D., Levy R. M., Kofke D., Yarmush M. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water. J. Comp. Chem. 11:1990;1169-1180.
    • (1990) J. Comp. Chem. , vol.11 , pp. 1169-1180
    • Kitchen, D.B.1    Hirata, F.2    Westbrook, J.D.3    Levy, R.M.4    Kofke, D.5    Yarmush, M.6
  • 22
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. J. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 23
    • 0026676167 scopus 로고
    • Sampling and efficiency of metric matrix distance geometry: A novel "partial" metrization algorithm
    • Kuszewski J., Nilges M., Brünger A. T. Sampling and efficiency of metric matrix distance geometry: a novel "partial" metrization algorithm. J. Biomol. NMR. 2:1992;33-56.
    • (1992) J. Biomol. NMR , vol.2 , pp. 33-56
    • Kuszewski, J.1    Nilges, M.2    Brünger, A.T.3
  • 24
    • 0023644998 scopus 로고
    • Structure of the C-terminal domain of the ribosomal protein L/L12 from Escherichia coli at 1.7 Å
    • Leijonmarck M., Liljas A. Structure of the C-terminal domain of the ribosomal protein L/L12 from Escherichia coli at 1.7 Å J. Mol. Biol. 195:1987;555-579.
    • (1987) J. Mol. Biol. , vol.195 , pp. 555-579
    • Leijonmarck, M.1    Liljas, A.2
  • 25
    • 0024330926 scopus 로고
    • Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5
    • Levy R. M., Bassolino D. A., Kitchen D. B., Pardi A. Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5. Biochemistry. 28:1989;9361-9372.
    • (1989) Biochemistry , vol.28 , pp. 9361-9372
    • Levy, R.M.1    Bassolino, D.A.2    Kitchen, D.B.3    Pardi, A.4
  • 27
    • 36449005845 scopus 로고
    • A deterministic global optimization method for molecular structure determination
    • Maranas C. D., Floudas C. A. A deterministic global optimization method for molecular structure determination. J. Chem. Phys. 100:1994a;1247-1261.
    • (1994) J. Chem. Phys. , vol.100 , pp. 1247-1261
    • Maranas, C.D.1    Floudas, C.A.2
  • 28
    • 0001203963 scopus 로고
    • Global minimum potential energy conformations of small molecules
    • Maranas C. D., Floudas C. A. Global minimum potential energy conformations of small molecules. J. Global Optimization. 4:1994b;135-170.
    • (1994) J. Global Optimization , vol.4 , pp. 135-170
    • Maranas, C.D.1    Floudas, C.A.2
  • 29
    • 0028897718 scopus 로고
    • Computer modeling of protein folding: Conformational and energetic analysis of reduced and detailed protein models
    • Monge A., Lathrop E., Gunn J., Shenkin P., Friesner R. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J. Mol. Biol. 247:1995;995-1012.
    • (1995) J. Mol. Biol. , vol.247 , pp. 995-1012
    • Monge, A.1    Lathrop, E.2    Gunn, J.3    Shenkin, P.4    Friesner, R.5
  • 30
    • 0028091859 scopus 로고
    • Refined X-ray structure of dictyostelium nucleoside diphosphate kinase at 1.8 Å resolution
    • Morera S., Lebras G., Lascu I., Lacombe M. L., Veron M., Janin J. Refined X-ray structure of dictyostelium nucleoside diphosphate kinase at 1.8 Å resolution. J. Mol. Biol. 243:1994;873-890.
    • (1994) J. Mol. Biol. , vol.243 , pp. 873-890
    • Morera, S.1    Lebras, G.2    Lascu, I.3    Lacombe, M.L.4    Veron, M.5    Janin, J.6
  • 31
    • 0024285896 scopus 로고
    • Determination of three-dimensional structures of proteins from interproton distance data by, hybrid distance geometry-dynamical simulated annealing calculations
    • Nilges M., Clore G. M., Gronenborn A. M. Determination of three-dimensional structures of proteins from interproton distance data by, hybrid distance geometry-dynamical simulated annealing calculations. FEBS Letters. 229:1988;317-324.
    • (1988) FEBS Letters , vol.229 , pp. 317-324
    • Nilges, M.1    Clore, G.M.2    Gronenborn, A.M.3
  • 33
    • 0028268603 scopus 로고
    • Synthetic structural and biological studies of the ubiquitin system. Part 1
    • Ramage R., Green J., Muir T. W., Ogunjobi O. M., Love S., Shaw K. Synthetic structural and biological studies of the ubiquitin system. Part 1. Biochem. J. 299:1994;151-158.
    • (1994) Biochem. J. , 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
  • 35
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Skolnick J., Kolinski A., Ortiz A. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265:1997;217-241.
    • (1997) J. Mol. Biol. , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.3
  • 36
    • 0027168790 scopus 로고
    • Global folding of proteins using a limited number of distance constraints
    • Smith-Brown M. J., Kominos D., Levy R. Global folding of proteins using a limited number of distance constraints. Protein Eng. 6:1993;605-614.
    • (1993) Protein Eng. , vol.6 , pp. 605-614
    • Smith-Brown, M.J.1    Kominos, D.2    Levy, R.3
  • 40
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:1986;230-252.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 41
    • 0023120307 scopus 로고
    • Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor
    • Wlodawer A., Deisenhofer J., Huber R. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. J. Mol. Biol. 193:1987;145-156.
    • (1987) J. Mol. Biol. , vol.193 , pp. 145-156
    • Wlodawer, A.1    Deisenhofer, J.2    Huber, R.3


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