Crossref journal-article
Elsevier BV
Progress in Biophysics and Molecular Biology (78)
Bibliography

Brunger, A. T., Adams, P. D., & Rice, L. M. (1999). Annealing in crystallography: a powerful optimization tool. Progress in Biophysics and Molecular Biology, 72(2), 135–155.

Authors 3
  1. Axel T. Brunger (first)
  2. Paul D. Adams (additional)
  3. Luke M. Rice (additional)
References 90 Referenced 23
  1. 10.1016/0022-2836(92)90936-E / J. Mol. Biol. / Optimal protocol and trajectory visualization for conformational searches of peptides and proteins by Abagyan (1992)
  2. {'key': '10.1016/S0079-6107(99)00004-8_BIB2', 'first-page': '896', 'volume': 'vol. 55', 'author': 'Abramowitz', 'year': '1968'} by Abramowitz (1968)
  3. 10.1073/pnas.94.10.5018 / Proc. Natl. Acad. Sci. USA / Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement by Adams (1997)
  4. 10.1107/S0907444998006635 / Acta Cryst. D / Extending the limits of molecular replacement through combined simulated annealing and maximum likelihood refinement by Adams (1999)
  5. 10.1021/ar00089a001 / Acc. Chem. Res. / Systematic analysis of structural data as a research technique in organic chemistry by Allen (1983)
  6. 10.1080/08905458708905124 / Mech. Struct. Mach. / A recursive formulation for constrained mechanical system dynamics. I. Open loop systems by Bae (1987)
  7. 10.1080/08905458708905130 / Mech. Struct. Mach. / A recursive formulation for constrained mechanical system dynamics. II. Open loop systems by Bae (1988)
  8. 10.1063/1.448118 / J. Chem. Phys. / Molecular dynamics with coupling to an external bath by Berendsen (1984)
  9. 10.1006/jmbi.1995.0360 / J. Mol. Biol. / Conformational variability of solution nuclear magnetic resonance structures by Bonvin (1995)
  10. 10.1007/BF00190458 / J. Biomol. NMR / Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? by Bonvin (1996)
  11. 10.1017/S0033583500004108 / Q. Rev. Biophys. / Distance geometry and related methods for protein structure determination from NMR data by Braun (1987)
  12. 10.1016/0022-2836(85)90134-2 / J. Mol. Biol. / Calculation of protein conformations by proton–proton distance constraints. A new efficient algorithm by Braun (1985)
  13. 10.1107/S010876739100541X / Acta Cryst. A / A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data by Bricogne (1991)
  14. 10.1107/S0907444992010400 / Acta Cryst. D / Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives by Bricogne (1993)
  15. 10.1016/S0076-6879(97)76069-5 / Meth. Enzy. / Bayesian statistical viewpoint on structure determination: basic concepts and examples by Bricogne (1997)
  16. 10.1016/0022-2836(88)90211-2 / J. Mol. Biol. / Crystallographic refinement by simulated annealing: application to a 2.8 Å resolution structure of aspartate aminotransferase by Brunger (1988)
  17. 10.1038/355472a0 / Nature / The free R value: a novel statistical quantity for assessing the accuracy of crystal structures by Brunger (1992)
  18. 10.1073/pnas.83.11.3801 / Proc. Natl. Acad. Sci. USA / Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin by Brunger (1986)
  19. 10.1126/science.235.4787.458 / Science / Crystallographic R factor refinement by molecular dynamics by Brunger (1987)
  20. 10.1107/S0108767388009195 / Acta Cryst. A / Crystallographic refinement by simulated annealing: application to a 1.5 Å resolution structure of crambin by Brunger (1989)
  21. 10.1107/S0108767390002355 / Acta Cryst. A / Slow-cooling protocols for crystallographic refinement by simulated annealing by Brunger (1990)
  22. 10.1126/science.8332897 / Science / Assessment of the quality of solution nuclear magnetic resonance structures by complete cross-validation by Brunger (1993)
  23. 10.1002/ijch.199400022 / Israel J. Chem. / Thermal motion and conformational disorder in protein crystal structures: comparison of multi-conformer and time-averaging models by Burling (1994)
  24. 10.1126/science.271.5245.72 / Science / Direct observation of protein solvation and discrete disorder with experimental crystallographic phases by Burling (1996)
  25. 10.1002/j.1460-2075.1986.tb04557.x / EMBO J. / The three-dimensional structure of a-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics by Clore (1986)
  26. 10.1021/bi00411a042 / Biochemistry / Refinement of the solution structure of the DNA dodecamer 5′d(CGCGPATTCGCG)2 containing a stable purine–thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics by Clore (1988)
  27. 10.1063/1.1681994 / J. Chem. Phys. / Computer simulation of multiple chain systems – the effect of density on the average chain dimension by Curro (1974)
  28. 10.1016/0959-440X(95)80011-5 / Curr. Opin. Struct. Biol. / Proteins at atomic resolution by Dauter (1995)
  29. 10.1107/S0567739471000986 / Acta Cryst. A / A real-space refinement procedure for proteins by Diamond (1971)
  30. 10.1107/S0108767391001071 / Acta Cryst. A / Accurate bond and angle parameters for X-ray structure refinement by Engh (1991)
  31. 10.1107/S0021889888009550 / J. Appl. Cryst. / Testing the method of crystallographic refinement using molecular dynamics by Fujinaga (1989)
  32. 10.1006/jmrb.1994.1061 / J. Magn. Res. B / The impact of direct refinement against three-bond HN–C alpha H coupling constants on protein structure determination by NMR by Garrett (1994)
  33. {'key': '10.1016/S0079-6107(99)00004-8_BIB34', 'series-title': 'Classical Mechanics', 'author': 'Goldstein', 'year': '1980'} / Classical Mechanics by Goldstein (1980)
  34. 10.1126/science.2396108 / Science / Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics by Gros (1990)
  35. 10.1016/0076-6879(85)15021-4 / Meth. Enzymol. / Stereochemically restrained refinement of macromolecular structures by Hendrickson (1985)
  36. 10.1126/science.1925561 / Science / Determination of macromolecular structures from anomalous diffraction of synchrotron radiation by Hendrickson (1991)
  37. {'key': '10.1016/S0079-6107(99)00004-8_BIB38', 'first-page': '750', 'article-title': 'Die Faltmolekülmethode – eine neue Methode zur Bestimmung der Kristallstruktur bei Ganz oder Teilweise bekannter Molekülstruktur', 'volume': '10', 'author': 'Hoppe', 'year': '1957', 'journal-title': 'Acta Cryst.'} / Acta Cryst. / Die Faltmolekülmethode – eine neue Methode zur Bestimmung der Kristallstruktur bei Ganz oder Teilweise bekannter Molekülstruktur by Hoppe (1957)
  38. 10.1038/266140a0 / Nature / Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 Å and sequence homology with porcine pepsin by Hsu (1977)
  39. 10.1016/S0021-9991(83)71106-X / J. Comp. Phys. / A fast recursive algorithm for molecular dynamics simulation by Jain (1983)
  40. 10.1107/S0108767390010224 / Acta Cryst. A / Improved methods for building protein models in electron density maps and the location of errors in these models by Jones (1991)
  41. 10.1016/0022-2836(85)90036-1 / J. Mol. Biol. / A protein structure from nuclear magnetic resonance data. lac repressor headpiece by Kaptein (1985)
  42. 10.1021/ja00901a059 / J. Am. Chem. Soc. / Vicinal proton coupling in nuclear magnetic resonance by Karplus (1963)
  43. 10.1038/347631a0 / Nature / Molecular dynamics simulations in biology by Karplus (1990)
  44. 10.1002/prot.340080411 / Proteins Structure Function Genetics / Refinement of the NMR structures for acyl carrier protein with scalar coupling data by Kim (1990)
  45. 10.1126/science.220.4598.671 / Science / Optimization by simulated annealing by Kirkpatrick (1983)
  46. 10.1016/S0969-2126(96)00097-4 / Structure / Cross-validation in crystallography: practice and applications by Kleywegt (1996)
  47. 10.1016/0022-2836(86)90295-0 / J. Mol. Biol. / Effect of anisotropy and anharmonicity on protein crystallographic refinement by Kuriyan (1986)
  48. 10.1002/prot.340100407 / Proteins / Exploration of disorder in protein structures by X-ray restrained molecular dynamics by Kuriyan (1991)
  49. 10.1006/jmrb.1995.1093 / J. Magn. Res. B / The impact of direct refinement against proton chemical shifts on protein structure determination by NMR by Kuszewski (1995)
  50. 10.1006/jmrb.1995.1017 / J. Magn. Res. B / The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR by Kuszewski (1995)
  51. 10.1002/pro.5560050609 / Prot. Sci. / Improving the quality of NMR and crystallographic structures by means of a conformational potential derived from structure databases by Kuszewski (1996)
  52. Laarhoven, P.J.M., Aarts, E.H.L. (Eds.), 1987. Simulated Annealing: Theory and Applications. Reidel, Dordrecht, p. 187
  53. 10.1107/S0907444992008886 / Acta Cryst. D / Automated refinement of protein models by Lamzin (1993)
  54. 10.1073/pnas.84.19.6611 / Proc. Natl. Acad. Sci. USA / Monte Carlo-minimization approach to the multiple-minima problem in protein folding by Li (1987)
  55. 10.1002/prot.340200304 / Proteins Structure Function Genetics / Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton–Euler inverse mass operator method for internal coordinate dynamics by Mathiowetz (1994)
  56. 10.1063/1.1699114 / J. Chem. Phys. / Equation of state calculations by fast computing machines by Metropolis (1953)
  57. 10.1007/BF00124347 / Comput. Aided Mol. Des. / Coupling constants again: experimental restraints in structure refinement by Mierke (1994)
  58. 10.1107/S0907444996012255 / Acta Cryst. D / Refinement of macromolecular structures by the maximum-likelihood method by Murshudov (1997)
  59. {'key': '10.1016/S0079-6107(99)00004-8_BIB60', 'first-page': '260', 'article-title': 'X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 Å resolution of the aspartic proteinase from Mucor pusillus', 'volume': '230', 'author': 'Newman', 'year': '1993', 'journal-title': 'J. Mol. Biol.'} / J. Mol. Biol. / X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 Å resolution of the aspartic proteinase from Mucor pusillus by Newman (1993)
  60. 10.1006/jmbi.1994.0053 / J. Mol. Biol. / Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulfide connectivities by Nilges (1995)
  61. 10.1016/S0959-440X(96)80027-3 / Curr. Opin. Struct. Biol. / Structure calculation from NMR data by Nilges (1996)
  62. 10.1016/0014-5793(88)80559-3 / FEBS Lett. / Determination of three dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms by Nilges (1988)
  63. 10.1016/0014-5793(88)81148-7 / FEBS Lett. / Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations by Nilges (1988)
  64. 10.1093/protein/2.1.27 / Protein Eng. / Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2 by Nilges (1988)
  65. {'key': '10.1016/S0079-6107(99)00004-8_BIB66', 'series-title': 'Sampling Properties of Simulated Annealing and Distance Geometry. Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy', 'first-page': '451', 'author': 'Nilges', 'year': '1991'} / Sampling Properties of Simulated Annealing and Distance Geometry. Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy by Nilges (1991)
  66. 10.1007/BF00211749 / J. Biomol. NMR / Chemical shifts and three-dimensional protein structures. by Oldfield (1995)
  67. 10.1107/S0108767396004370 / Acta Cryst. A / Improved structure refinement through maximum likelihood by Pannu (1996)
  68. 10.1107/S0907444998004119 / Acta Cryst. D / Incorporation of prior phase information strengthens maximum likelihood structural refinement by Pannu (1998)
  69. 10.1107/S0907444995011115 / Acta Cryst. D / New parameters for the refinement of nucleic acid containing structures by Parkinson (1996)
  70. 10.1016/0022-2836(90)90019-I / J. Mol. Biol. / Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data by Pearlman (1990)
  71. 10.1107/S0907444997005696 / Acta Cryst. D / wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models by Perrakis (1997)
  72. {'key': '10.1016/S0079-6107(99)00004-8_BIB74', 'series-title': 'Numerical Recipes', 'first-page': '498', 'author': 'Press', 'year': '1986'} / Numerical Recipes by Press (1986)
  73. 10.1107/S0108767386099622 / Acta Cryst. A / Improved Fourier coefficients for maps using phases from partial structures with errors by Read (1986)
  74. 10.1107/S0108767390005529 / Acta Cryst. A / Structure-factor probabilities for related structures by Read (1990)
  75. 10.1002/prot.340190403 / Proteins Structure Function Genetics / Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement by Rice (1994)
  76. 10.1107/S0021889898006645 / J. Appl. Cryst. / Phase improvement by multi-start simulated annealing refinement and structure factor averaging by Rice (1998)
  77. 10.1107/S0365110X62000067 / Acta Cryst. A / The detection of sub-units within the crystallographic asymmetric unit by Rossmann (1962)
  78. 10.1021/ja00244a051 / J. Am. Chem. Soc. / Stochastic exploration of molecular mechanics energy surfaces: hunting for the global minimum by Saunders (1987)
  79. 10.1107/S0907444995007669 / Acta Cryst. D / Ribonuclease from Streptomyces aureofaciens at atomic resolution by Sevcik (1996)
  80. 10.1038/nsb0397-215 / Nat. Struct. Biol. / Crystal structure of the two RNA-binding domains of human hnRNP A1 at 1.75 Å resolution by Shamoo (1997)
  81. 10.1107/S0108768185001781 / Acta Cryst. B / The refinement of southern bean mosaic virus in reciprocal space by Silva (1985)
  82. 10.1107/S0907444994014484 / Acta Cryst. D / Full-matrix refinement of the protein crambin at 0.83 Å and 130 K by Stec (1995)
  83. 10.1006/jmre.1996.1027 / J. Magn. Reson. B / Torsion angle molecular dynamics is a new, efficient tool for NMR structure calculation by Stein (1997)
  84. 10.1107/S0567739477001958 / Acta Cryst. A / Structure-factor least-squares refinement procedure for macromolecular structure using constrained and restrained parameters by Sussman (1977)
  85. 10.1007/BF00174609 / J. Biomol. NMR / Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: an alternative method for generating a high-resolution solution structure by Ulyanov (1993)
  86. 10.1103/PhysRev.159.98 / Phys. Rev. / Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules by Verlet (1967)
  87. 10.1107/S0907444998002492 / Acta Cryst. D / Structural parameters for proteins derived from the atomic resolution (1.09 Å) structure of a designed variant of the colE1 ROP protein by Vlassi (1998)
  88. 10.1016/0022-2836(90)90234-D / J. Mol. Biol. / Refinement of the influenza virus haemagglutinin by simulated annealing by Weis (1989)
  89. {'key': '10.1016/S0079-6107(99)00004-8_BIB91', 'series-title': 'NMR of Proteins and Nucleic Acids', 'author': 'Wüthrich', 'year': '1986'} / NMR of Proteins and Nucleic Acids by Wüthrich (1986)
  90. 10.1006/jmrb.1995.1123 / J. Mag. Res. B / Structure determination from NOESY intensities using a metropolis simulated-annealing (MSA) refinement of dihedral angles by Xu (1995)
Dates
Type When
Created 23 years, 1 month ago (July 25, 2002, 7:39 p.m.)
Deposited 1 year, 10 months ago (Oct. 26, 2023, 8:30 a.m.)
Indexed 2 months, 1 week ago (June 20, 2025, 5:22 p.m.)
Issued 26 years ago (Aug. 1, 1999)
Published 26 years ago (Aug. 1, 1999)
Published Print 26 years ago (Aug. 1, 1999)
Funders 0

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@article{Brunger_1999, title={Annealing in crystallography: a powerful optimization tool}, volume={72}, ISSN={0079-6107}, url={http://dx.doi.org/10.1016/s0079-6107(99)00004-8}, DOI={10.1016/s0079-6107(99)00004-8}, number={2}, journal={Progress in Biophysics and Molecular Biology}, publisher={Elsevier BV}, author={Brunger, Axel T. and Adams, Paul D. and Rice, Luke M.}, year={1999}, month=aug, pages={135–155} }