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Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

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Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. / DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas C; Cheng, Yifan; Baker, David.

In: NAT METHODS, Vol. 12, No. 4, 04.2015, p. 361-5.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

DiMaio, F, Song, Y, Li, X, Brunner, MJ, Xu, C, Conticello, V, Egelman, E, Marlovits, TC, Cheng, Y & Baker, D 2015, 'Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement', NAT METHODS, vol. 12, no. 4, pp. 361-5. https://doi.org/10.1038/nmeth.3286

APA

DiMaio, F., Song, Y., Li, X., Brunner, M. J., Xu, C., Conticello, V., Egelman, E., Marlovits, T. C., Cheng, Y., & Baker, D. (2015). Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. NAT METHODS, 12(4), 361-5. https://doi.org/10.1038/nmeth.3286

Vancouver

DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V et al. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. NAT METHODS. 2015 Apr;12(4):361-5. https://doi.org/10.1038/nmeth.3286

Bibtex

@article{352f3a660f1d4ffaa87067a9f9aa938e,
title = "Atomic-accuracy models from 4.5-{\AA} cryo-electron microscopy data with density-guided iterative local refinement",
abstract = "We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-{\AA} resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.",
keywords = "Chemistry, Physical, Cryoelectron Microscopy, Models, Molecular, Monte Carlo Method, Proteins",
author = "Frank DiMaio and Yifan Song and Xueming Li and Brunner, {Matthias J} and Chunfu Xu and Vincent Conticello and Edward Egelman and Marlovits, {Thomas C} and Yifan Cheng and David Baker",
year = "2015",
month = apr,
doi = "10.1038/nmeth.3286",
language = "English",
volume = "12",
pages = "361--5",
journal = "NAT METHODS",
issn = "1548-7091",
publisher = "NATURE PUBLISHING GROUP",
number = "4",

}

RIS

TY - JOUR

T1 - Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement

AU - DiMaio, Frank

AU - Song, Yifan

AU - Li, Xueming

AU - Brunner, Matthias J

AU - Xu, Chunfu

AU - Conticello, Vincent

AU - Egelman, Edward

AU - Marlovits, Thomas C

AU - Cheng, Yifan

AU - Baker, David

PY - 2015/4

Y1 - 2015/4

N2 - We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.

AB - We describe a general approach for refining protein structure models on the basis of cryo-electron microscopy maps with near-atomic resolution. The method integrates Monte Carlo sampling with local density-guided optimization, Rosetta all-atom refinement and real-space B-factor fitting. In tests on experimental maps of three different systems with 4.5-Å resolution or better, the method consistently produced models with atomic-level accuracy largely independently of starting-model quality, and it outperformed the molecular dynamics-based MDFF method. Cross-validated model quality statistics correlated with model accuracy over the three test systems.

KW - Chemistry, Physical

KW - Cryoelectron Microscopy

KW - Models, Molecular

KW - Monte Carlo Method

KW - Proteins

U2 - 10.1038/nmeth.3286

DO - 10.1038/nmeth.3286

M3 - SCORING: Journal article

C2 - 25707030

VL - 12

SP - 361

EP - 365

JO - NAT METHODS

JF - NAT METHODS

SN - 1548-7091

IS - 4

ER -