Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing
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Ashton, 1997, Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses, J. Mol. Biol., 272, 408, 10.1006/jmbi.1997.1271
Ban, 1998, A 9Å resolution X-ray crystallographic map of the large ribosomal subunit, Cell, 93, 1105, 10.1016/S0092-8674(00)81455-5
Berglund, 1997, Solution structure of the ribosomal RNA binding protein S15 from Th. thermophilus, Nat. Struct. Biol., 4, 20, 10.1038/nsb0197-20
Bilgin, 1998, Solution structure of the ternary complex between aminoacyl-tRNA, elongation factor Tu, and guanosine triphosphate, Biochemistry, 37, 8163, 10.1021/bi9802869
Bernstein, 1977, The Protein Data Bank: a computer-based archival file for macromolecular structures, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3
Boulin, 1986, Data appraisal, evaluation and display for synchrotron radiation experiments: hardware and software, Nucl. Instrum. Meth., A249, 399, 10.1016/0168-9002(86)90694-7
Boulin, 1988, Data acquisition systems for linear and area X-ray detectors using delay line readout, Nucl. Instrum. Meth., A269, 312, 10.1016/0168-9002(88)90895-9
Capel, 1987, A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli, Science, 238, 1403, 10.1126/science.3317832
Chacón, 1998, Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm, Biophys. J., 74, 2760, 10.1016/S0006-3495(98)77984-6
Davies, 1996, The crystal structure of ribosomal protein S8: implications for modelling the central domain of 16A rRNA, Structure, 4, 1093, 10.1016/S0969-2126(96)00115-3
Feigin, 1987
Frank, 1995, A model of protein synthesis based on a new cryo-electron microscopy reconstruction of the E. coli ribosome, Nature, 376, 441, 10.1038/376441a0
Frieden, 1971, Evaluation, design and extrapolation methods for optical signals, based on the use of the prolate functions, 9, 312
Gabriel, 1982, The localization method used at EMBL, Nucl. Instrum. Meth., 201, 223, 10.1016/0167-5087(82)90031-X
Ingber, 1993, Simulated annealing: practice versus theory, Math. Computer Modelling, 18, 29, 10.1016/0895-7177(93)90204-C
Kirkpatrick, 1983, Optimization by simulated annealing, Science, 220, 671, 10.1126/science.220.4598.671
Kjeldgaard, 1993, The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation, Structure, 1, 35, 10.1016/0969-2126(93)90007-4
Koch, 1979, Neutron scattering studies of ribosomes, Meth. Enzymol., 59, 670, 10.1016/0076-6879(79)59121-6
Kozin, 1997, ASSA: a program for three-dimensional rendering in solution scattering from biopolymers, J. Appl. Crystallogr., 30, 811, 10.1107/S0021889897001830
Krueger, 1997, Structures of calmodulin and a functional myosin light chain kinase in the activated complex: a neutron scattering study, Biochemistry, 36, 6017, 10.1021/bi9702703
May, 1992, Inter-protein distances within the large subunit from Escherichia coli ribosomes, EMBO J., 11, 373, 10.1002/j.1460-2075.1992.tb05060.x
Moore, 1980, Small-angle scattering. Information content and error analysis, J. Appl. Cryst, 13, 168, 10.1107/S002188988001179X
Porod, 1982, General theory, 17
Press, 1992
Ramakrishnan, 1992, The structure of ribosomal protein S5 reveals 2 sites of interaction with 16S RNA, Nature, 358, 768, 10.1038/358768a0
Schönbrunn, 1998, Studies on the conformational changes in the bacterial cell wall biosynthetic enzyme UDP-N-acetylglucosamine enolpyruvyltransferase (MurA), Eur. J. Biochem., 253, 406, 10.1046/j.1432-1327.1998.2530406.x
Shannon, 1949
Skarzynski, 1996, Structure of UDP-n-Acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-n-Acetylglucosamine and the drug fosfomycin, Structure, 4, 1465, 10.1016/S0969-2126(96)00153-0
Stuhrmann, 1970, Ein neues Verfahren zur Bestimmung der Oberflächenform und der inneren Struktur von gelösten globulären Proteinen aus Röntgenkleinwinkelmessungen, Zeitschr. Physik. Chem. Neue Folge, 72, 177, 10.1524/zpch.1970.72.4_6.177
Stuhrmann, 1970, Interpretation of small-angle scattering of dilute solutions and gases. A representation of the structures related to a one-particle scattering functions, Acta Crystallogr., A26, 297, 10.1107/S0567739470000748
Stuhrmann, 1965, Elimination der intrapartikulären Untergrundstreuung bei der Röntgenkleinwinkelstreuung am kompakten Teilchen (Proteinen), Zeitschr. Physik. Chem. Neue Folge, 46, 247, 10.1524/zpch.1965.46.3_4.247
Svergun, 1993, A direct indirect method of small-angle scattering data treatment, J. Appl. Crystallogr., 26, 258, 10.1107/S0021889892011828
Svergun, 1994, Solution scattering from biopolymers: advanced contrast variation data analysis, Acta Crystallogr., A50, 391, 10.1107/S0108767393013492
Svergun, 1991, New developments in direct shape determination from small-angle scattering. 1. Theory and model calculations, Acta Crystallogr., A47, 736, 10.1107/S0108767391006414
Svergun, 1995, CRYSOL: a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates, J. Appl. Crystallogr., 28, 768, 10.1107/S0021889895007047
Svergun, 1996, New developments in direct shape determination from small-angle scattering. 2. Uniqueness, Acta Crystallogr., A52, 419, 10.1107/S0108767396000177
Svergun, 1997, Shape determination from solution scattering of biopolymers, J. Appl. Crystallogr., 30, 798, 10.1107/S0021889897001714
Svergun, 1997, Solution scattering structural analysis of the 70S Escherichia coli ribosome by contrast variation, J. Mol. Biol., 271, 588, 10.1006/jmbi.1997.1190
Svergun, 1998, A model of the quaternary structure of the Escherichia coli F1 ATPase from X-ray solution scattering and evidence for structural changes in the δ subunit during ATP hydrolysis, Biophys. J., 75, 2212, 10.1016/S0006-3495(98)77665-9
Svergun, 1998, Protein hydration in solution: experimental observation by X-ray and neutron scattering, Proc. Natl. Acad. Sci. USA, 95, 2267, 10.1073/pnas.95.5.2267
Taupin, 1982, Informational content and retrieval in solution scattering studies. I. Degrees of freedom and data reduction, J. Appl. Crystallogr., 15, 289, 10.1107/S0021889882012011
Waksman, 1994, Crystal structure of Escherichia coli thioredoxin reductase refined at 2 angstrom resolution: implications for a large conformational change during catalysis, J. Mol. Biol., 236, 800, 10.1006/jmbi.1994.1190