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将多元函数的变尺度法与两电子密度图的相关系数相结合,得到一种能够对蛋白质晶体结构进行刚体优化的新方法.初步测试结果表明,该方法能够明显地改善待测晶体的初始模型在晶胞中的取向和位置.而与最大似然方法相比,该方法可能更适用于搜索空间中存在大量局域极值点的情况.
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关键词:
- 蛋白质晶体结构 /
- 刚体优化 /
- 多元函数的变尺度方法 /
- 电子密度图的相关系数
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:
- protein crystal structures /
- rigid-body refinement /
- variable metric methods in multidimensions /
- the electron density map correlation coefficient
[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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[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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