Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient

doi:10.1088/1674-1056/19/10/106101

Abstract A previously published new rotation function has been improved by using a dynamic correlation coefficient as well as two new scoring functions of relative entropy and mean-square-residues to make the rotation function more robust and independent of a specific set of weights for scoring and ranking. The previously described new rotation function calculates the rotation function of molecular replacement by matching the search model directly with the Patterson vector map. The signal-to-noise ratio for the correct match was increased by averaging all the matching peaks. Several matching scores were employed to evaluate the goodness of matching. These matching scores were then combined into a single total score by optimizing a set of weights using the linear regression method. It was found that there exists an optimal set of weights that can be applied to the global rotation search and the correct solution can be ranked in the top 100 or less. However, this set of optimal weights in general is dependent on the search models and the crystal structures with different space groups and cell parameters. In this work, we try to solve this problem by designing a dynamic correlation coefficient. It is shown that the dynamic correlation coefficient works for a variety of space groups and cell parameters in the global search of rotation function. We also introduce two new matching scores: relative entropy and mean-square-residues. Last but not least, we discussed a valid method for the optimization of the adjustable parameters for matching vectors.

Keywords: molecular replacement rotation function global search correlation coefficient

Received: 26 April 2010
Revised: 10 May 2010
Accepted manuscript online:

PACS:	61.50.Ah	(Theory of crystal structure, crystal symmetry; calculations and modeling)
	61.66.-f	(Structure of specific crystalline solids)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 10674172 and 10874229).

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Jiang Fan(江凡) and Ding Wei(丁玮) Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient 2010 Chin. Phys. B 19 106101

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Improvement of a new rotation function for molecular replacement by designing new scoring functions and dynamic correlation coefficient

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