Author:
Miyaguchi Ikuko,Sato Miwa,Kashima Akiko,Nakagawa Hiroyuki,Kokabu Yuichi,Ma Biao,Matsumoto Shigeyuki,Tokuhisa Atsushi,Ohta Masateru,Ikeguchi Mitsunori
Abstract
AbstractLow-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, called quality assessment based on an electron density map (QAEmap), which evaluates local protein structures determined by X-ray crystallography and could be applied to correct structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and putative high-resolution experimental electron density map. This correlation could be used as a metric to modify the structure. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.
Publisher
Springer Science and Business Media LLC
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