Article

Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

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Abstract

Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices.

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... The number of detected amino acids and 2-way distance are two parameters that have been used previously in accuracy measurement. Length-association method was proposed recently and can be a potentially more sensitive method to evaluate secondary structure detection [45]. ...
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