DeepAlign, a 3D Alignment Method based on Regionalized Deep Learning for Cryo-EM

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F21%3A00121351" target="_blank" >RIV/00216224:14610/21:00121351 - isvavai.cz</a>

Result on the web

<a href="https://www.sciencedirect.com/science/article/pii/S1047847721000174" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1047847721000174</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.jsb.2021.107712" target="_blank" >10.1016/j.jsb.2021.107712</a>

Result language

angličtina

Original language name

DeepAlign, a 3D Alignment Method based on Regionalized Deep Learning for Cryo-EM

Original language description

Cryo Electron Microscopy (Cryo-EM) is currently one of the main tools to reveal the structural information of biological specimens at high resolution. Despite the great development of the techniques involved to solve the biological structures with Cryo-EM in the last years, the reconstructed 3D maps can present lower resolution due to errors committed while processing the information acquired by the microscope. One of the main problems comes from the 3D alignment step, which is an error-prone part of the reconstruction workflow due to the very low signal-to-noise ratio (SNR) common in Cryo-EM imaging. In fact, as we will show in this work, it is not unusual to find a disagreement in the alignment parameters in approximately 20–40% of the processed images, when outputs of different alignment algorithms are compared. In this work, we present a novel method to align sets of single particle images in the 3D space, called DeepAlign. Our proposal is based on deep learning networks that have been successfully used in plenty of problems in image classification. Specifically, we propose to design several deep neural networks on a regionalized basis to classify the particle images in sub-regions and, then, make a refinement of the 3D alignment parameters only inside that sub-region. We show that this method results in accurately aligned images, improving the Fourier shell correlation (FSC) resolution obtained with other state-of-the-art methods while decreasing computational time.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

—

Continuities

S - Specificky vyzkum na vysokych skolach

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Structural Biology

ISSN

1047-8477

e-ISSN

1095-8657

Volume of the periodical

213

Issue of the periodical within the volume

2

Country of publishing house

US - UNITED STATES

Number of pages

14

Pages from-to

„107712“

UT code for WoS article

000756475200010

EID of the result in the Scopus database

2-s2.0-85102652992