DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM

Author:

Al-Azzawi Adil,Ouadou Anes,Max Highsmith,Duan Ye,Tanner John J.,Cheng JianlinORCID

Abstract

Abstract Background Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio of micrographs. Because of these issues, significant human intervention is often required to generate a high-quality set of particles for input to the downstream structure determination steps. Results Here we propose a fully automated approach (DeepCryoPicker) for single particle picking based on deep learning. It first uses automated unsupervised learning to generate particle training datasets. Then it trains a deep neural network to classify particles automatically. Results indicate that the DeepCryoPicker compares favorably with semi-automated methods such as DeepEM, DeepPicker, and RELION, with the significant advantage of not requiring human intervention. Conclusions Our framework combing supervised deep learning classification with automated un-supervised clustering for generating training data provides an effective approach to pick particles in cryo-EM images automatically and accurately.

Funder

National Science Foundation

National Institutes of Health

National Institute of General Medical Sciences

Publisher

Springer Science and Business Media LLC

Subject

Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology

Cited by 37 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

1. CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net;Briefings in Bioinformatics;2024-05-23

2. Deep Learning Recognition of Wheat Leaf Disease Using MobileNetV2 Model;2024 4th International Conference on Innovative Research in Applied Science, Engineering and Technology (IRASET);2024-05-16

3. Cryo-electron microscopy-based drug design;Frontiers in Molecular Biosciences;2024-03-04

4. CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs;Bioinformatics;2024-02-24

5. Operative features of CNN layers characterizing deep learning;AIP Conference Proceedings;2024

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3