EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps

Abstract The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilde...

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Autores principales:	Niyun Zhou, Hongwei Wang, Jiawei Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/79ab52c3922a4eda8cb40a1b7d751ccc
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spelling	oai:doaj.org-article:79ab52c3922a4eda8cb40a1b7d751ccc2021-12-02T16:06:36ZEMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps10.1038/s41598-017-02725-w2045-2322https://doaj.org/article/79ab52c3922a4eda8cb40a1b7d751ccc2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02725-whttps://doaj.org/toc/2045-2322Abstract The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.Niyun ZhouHongwei WangJiawei WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Niyun Zhou Hongwei Wang Jiawei Wang EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
description	Abstract The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.
format	article
author	Niyun Zhou Hongwei Wang Jiawei Wang
author_facet	Niyun Zhou Hongwei Wang Jiawei Wang
author_sort	Niyun Zhou
title	EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
title_short	EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
title_full	EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
title_fullStr	EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
title_full_unstemmed	EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
title_sort	embuilder: a template matching-based automatic model-building program for high-resolution cryo-electron microscopy maps
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/79ab52c3922a4eda8cb40a1b7d751ccc
work_keys_str_mv	AT niyunzhou embuilderatemplatematchingbasedautomaticmodelbuildingprogramforhighresolutioncryoelectronmicroscopymaps AT hongweiwang embuilderatemplatematchingbasedautomaticmodelbuildingprogramforhighresolutioncryoelectronmicroscopymaps AT jiaweiwang embuilderatemplatematchingbasedautomaticmodelbuildingprogramforhighresolutioncryoelectronmicroscopymaps
_version_	1718384970307731456

EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps

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