A new method of rigid-body refinementfor protein crystal structures

Ding Wei; Jiang Fan

doi:10.7498/aps.60.046103

Abstract

A new rigid-body refinement method for protein crystal structures is described. It is based on "Variable Metric Methods in Multidimensions" and "the Electron Density Map Correlation Coefficient". Test shows that the orientation and translation of the initial models can be improved effectively by this new method. And it can escape from the local extremum and reach the global optimum more easily than the maximum likelihood method when the search space has a large number of local extremum points.

Keywords:

Authors and contacts

Ding Wei,
Jiang Fan

1.
Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

References

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Cited By

[1]	Trapani S, Navaza J 2008 Acta Cryst. D 64 11
[2]	Cohen S X, Ben Jelloul M, Long F, Vagin A, Knipscheer P, Lebbink J, Sixma T K, Lamzin V S, Murshudov G N, Perrakis A 2008 Acta Cryst. D 64 49
[3]	Long F, Vagin A A, Young P, Murshudov G N 2008 Acta Cryst. D 64 125
[4]	Vagin A, Teplyakov A 2010 Acta Cryst. D 66 22
[5]	Keegan R M, Winn M D 2008 Acta Cryst. D 64 119
[6]	McCoy A J, Grosse-Kunstleve R W, Adams P D, Winn M D, Storoni L C, Read R J 2007 J. Appl. Cryst. 40 658
[7]	Schwarzenbacher R, Godzik A, Jaroszewski L 2008 Acta Cryst. D 64 133
[8]	Konnert J 1976 Acta Cryst. A 32 614
[9]	Brunger A T, Adams P D, Rice L M 2006 International Tables for Crystallography F 375
[10]	Murshudov G N, Vagin A A, Dodson E J 1997 Acta Cryst. D 53 240
[11]	Press W, Teukolsky S, Vetterling W, Flannery B 1992 Numerical recipes in C Cambridge university press Cambridge p425
[12]	Lunin V Y, Woolfson M M 1993 Acta Cryst. D 49 530
[13]	Jiang F 2008 Acta Cryst. D 64 561
[14]	Jiang F, Ding W 2010 Chin. Phys. B 19 106101
[15]	Drenth J, Mesters J 2007 Principles of protein X-ray crystallography 3rd ed. Springer New York p84
[16]	Bailey S 1994 Acta Cryst. D 50 760
[17]	Upstill C 1988 Nature 333 613
[18]	Shoemake K 1985 SIGGRAPH Comput. Graph. 19 245
[19]	Ueno T, Koshiyama T, Ohashi M, Kondo K, Kono M, Suzuki A, Yamane T, Watanabe Y 2005 J. Am. Chem. Soc 127 6556
[20]	Vojtechovsky J, Chu K, Berendzen J, Sweet R M, Schlichting I 1999 Biophys. J. 77 2153
[21]	Zhang T, Wu L J, Gu Y X, Zheng C D, Fan H F 2010 Chin. Phys. B 19 096101
[22]	Zhang T, Wu L J, Gu Y X, Zheng C D, Fan H F 2010 Chin. Phys. B 19 086103
[23]	Bao W X, Zhu C C, Cui W Z 2005 Acta Phys. Sin. 54 5281 (in Chinese) [保文星、朱长纯、崔万照 2005 54 5281]
[24]	Liang W X, Zhang J J, Lu J F, Liao R 2001 Chin. Phys. 10 1129

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Catalog

Vol. 60, Issue 4 - 2011-02-20

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