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Title: Cryo_fit: Democratization of flexible fitting for cryo-EM

Abstract

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.

Authors:
 [1];  [2];  [3];  [2];  [2];  [2];  [4];  [5]
+ Show Author Affiliations
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. New York Univ., Abu Dhabi (United Arab Emirates)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH)
OSTI Identifier:
1673369
Alternate Identifier(s):
OSTI ID: 1702027; OSTI ID: 1845294
Report Number(s):
LA-UR-19-31082
Journal ID: ISSN 1047-8477
Grant/Contract Number:  
89233218CNA000001; R01-GM072686; P01-GM063210; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Structural Biology
Additional Journal Information:
Journal Volume: 208; Journal Issue: 1; Journal ID: ISSN 1047-8477
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cryo_EM; molecular dynamics; flexible fitting; correlation coefficient; Phenix

Citation Formats

Kim, Doo Nam, Moriarty, Nigel W., Kirmizialtin, Serdal, Afonine, Pavel V., Poon, Billy, Sobolev, Oleg V., Adams, Paul D., and Sanbonmatsu, Karissa. Cryo_fit: Democratization of flexible fitting for cryo-EM. United States: N. p., 2019. Web. doi:10.1016/j.jsb.2019.05.012.
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Kim, Doo Nam, Moriarty, Nigel W., Kirmizialtin, Serdal, Afonine, Pavel V., Poon, Billy, Sobolev, Oleg V., Adams, Paul D., & Sanbonmatsu, Karissa. Cryo_fit: Democratization of flexible fitting for cryo-EM. United States. https://doi.org/10.1016/j.jsb.2019.05.012
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Kim, Doo Nam, Moriarty, Nigel W., Kirmizialtin, Serdal, Afonine, Pavel V., Poon, Billy, Sobolev, Oleg V., Adams, Paul D., and Sanbonmatsu, Karissa. Wed . "Cryo_fit: Democratization of flexible fitting for cryo-EM". United States. https://doi.org/10.1016/j.jsb.2019.05.012. https://www.osti.gov/servlets/purl/1673369.
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@article{osti_1673369,
title = {Cryo_fit: Democratization of flexible fitting for cryo-EM},
author = {Kim, Doo Nam and Moriarty, Nigel W. and Kirmizialtin, Serdal and Afonine, Pavel V. and Poon, Billy and Sobolev, Oleg V. and Adams, Paul D. and Sanbonmatsu, Karissa},
abstractNote = {Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.},
doi = {10.1016/j.jsb.2019.05.012},
journal = {Journal of Structural Biology},
number = 1,
volume = 208,
place = {United States},
year = {Wed Jul 03 00:00:00 EDT 2019},
month = {Wed Jul 03 00:00:00 EDT 2019}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1016/j.jsb.2019.05.012
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Figures / Tables:

Figure 1 Figure 1: Comparison of different programs for adenylate kinase (PDB code 1ake, 4ake) atomic model fitting.
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    Works referencing / citing this record:

    Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps
    journal, December 2019

    Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps
    journal, December 2019

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