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

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

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

Projekt

—

Návaznosti

S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2021

Kód důvěrnosti údajů

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

Název periodika

Journal of Structural Biology

ISSN

1047-8477

e-ISSN

1095-8657

Svazek periodika

213

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

14

Strana od-do

„107712“

Kód UT WoS článku

000756475200010

EID výsledku v databázi Scopus

2-s2.0-85102652992