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ESCET: A tool for including coordinate uncertainties into structure comparisons

Thomas R. Schneider
FIRC Institute of Molecular Oncology,
Via Adamello, 16, 20139 Milan, Italy

Coordinate uncertainties in crystal structures of biological macromolecules can vary from 0.01 Å for a well determined atom in a high-resolution structure to 1 Å for a mobile atom in a structure determined at low resolution. Given this wide range, it is important to take into account the coordinate uncertainties in particular in the comparison of structural models to discriminate significant differences from differences due to noise.

After normalization to their errors, difference distance matrices [1] allow to objectively access similarities and differences between structural models without any explicit superposition. Recently, a genetic algorithm that rapidly interprets large sets of such matrices in order to identify the part of the molecule that is conformationally invariant with respect to a possibly large set of conformers has been implemented in a computer program called 'ESCET' [2] and its functionality has been demonstrated [3].

The heuristic estimates of coordinate uncertainties used in the program that are based on Cruickshank's “Diffraction Precision Indicator” [4] will be described and some representative applications of the method will be discussed.

[1] Schneider, Acta Cryst. (2000) D56, 714-721
[2] http://www.escet.org.
[3] Schneider, Acta Cryst. (2002) D58, 195-208
[4] Cruickshank, Acta Cryst. (1999) D55 ,583-601