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Cited by 295Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and DynamicsEnzyme Structure and Function

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

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DiMaio, Frank, Tyka, Michael D., Baker, Matthew L., Chiu, Wah, Baker, David·2009·Journal of Molecular Biology
DOI 10.1016/j.jmb.2009.07.008PMC PMC3899897
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Abstract

We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy of starting models generated either by comparative modeling or by hand-tracing the density. The method can achieve near-atomic resolution starting from density maps at 4-6 A resolution.

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Crossref · 10.1016/j.jmb.2009.07.008

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  • Coot primarily uses a real-space refinement system that only respects local geometry, whereas the Rosetta force field used by Foldit is much more extensive, including additional steric, electrostatic and solvation terms, as well as statistical potentials based on observed backbone torsions and side-chain rotamers.

    “Whereas Coot primarily uses a real-space refinement system15 that only respects local geometry, the Rosetta force field used by Foldit is much more extensive, including additional steric, electrostatic and solvation terms, as well as statistical potentials based on observed backbone torsions and side-chain rotamers6.”

    From Determining crystal structures through crowdsourcing and coursework (2016) · cites this paper as [6]

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Cites

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Research works printed but not linked: 25

  1. [1]Jiang W Baker ML Ludtke SJ Chiu W 2001 Bridging the information gap: Computational tools for intermediate resolution structure interpretation J Mol Bio 308 1033 1044 11352589
  2. [2]Cowtan K 1998 Modified phased translation functions and their application to molecular fragment location Acta Cryst D 54 750 756 9757089
  3. [4]Topf M Baker ML Marti-Renoma MA Chiu W Sali A 2006 Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting J Mol Bio 357 1655 1668 16490207
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  5. [6]Orzechowski M Tama F 2008 Flexible fitting of high-resolution X-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations Biophys J 95 5692 5705 18849406 PMC2599853
  6. [7]Schröder G Brunger A Levitt M 2007 Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution Structure 15 1630 1641 18073112 PMC2213367
  7. [8]Tama F Miyashita O Brooks CL III 2004 Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis J Mol Biol 337 985 999 15033365
  8. [9]Jolley CC Wells SA Fromme P Thorpe MF 2008 Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations Biophys J 94 1613 21 17993504 PMC2242741
  9. [10]Velazquez-Muriel JA Valle M Santamaría-Pang A Kakadiaris IA Carazo JM 2006 Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies Structure 14 1115 1126 16843893
  10. [11]Topf M Lasker K Webb B Wolfson H Chiu W Sali A 2008 Protein structure fitting and refinement guided by cryo-EM density Structure 16 295 307 18275820 PMC2409374
  11. [12]Bradley P Misura KM Baker D 2005 Toward high-resolution de novo structure prediction for small proteins Science 309 1868 1871 16166519
  12. [13]Rohl CA 2005 Protein structure estimation using Rosetta NMR Meth Enz 394 244 260 15808223
  13. [14]John B Sali A 2003 Comparative protein structure modeling by iterative alignment, model building and model assessment Nucl Acids Res 31 3982 3992 12853614 PMC165975
  14. [15]Zhou H Baker ML Jiang W Dougherty M Jakana J Dong G Lu G Chiu W 2001 Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus Nat Struct Biol 8 868 873 11573092
  15. [16]Nakagawa A Miyazaki N Taka J Naitow H Ogawa A Fujimoto Z Mizuno H Higashi T Watanabe Y Omura T Cheng RH Tsukihara T 2003 The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins Structure 11 1227 1238 14527391
  16. [17]McGuffin LJ Jones DT 2003 Improvement of the GenTHREADER method for genomic fold recognition Bioinformatics 19 874 881 12724298
  17. [18]Grimes J Basak AK Roy P Stuart D 1995 The crystal structure of bluetongue virus VP7 Nature 373 167 170 7816101
  18. [19]Ludtke SJ Baker ML Chen DH Song JL Chuang DT Chiu W 2008 De novo backbone trace of GroEL from single particle electron cryomicroscopy Structure 16 441 448 18334219
  19. [20]Baker ML Ju T Chiu W 2007 Identification of secondary structure elements in intermediate-resolution density maps Structure 15 7 19 17223528 PMC1810566
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Cited by

Sorted by citations

Authors
DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D.
Affiliations
  • University of Washington (US)
  • Baylor College of Medicine (US)
Corresponding author
  • DiMaio, Frank
  • Baker, Matthew L.
  • Baker, David
ORCID
Venue
Journal of Molecular Biology
Publisher
Elsevier BV
Published
2009-09
Volume
392
Issue
1
Pages
181-190
ISSN
0022-2836 (ISSN-L)
DOI
10.1016/j.jmb.2009.07.008
PMC
PMC3899897
OpenAlex
W1985145180
Cited by
295
References
0
Citations by year
2026: 9 · 2025: 11 · 2024: 10 · 2023: 12 · 2022: 22 · 2021: 11 · 2020: 19 · 2019: 15 · 2018: 22 · 2017: 22 · 2016: 22 · 2015: 24 · 2014: 16 · 2013: 32 · 2012: 20
FWCI
9.21
Type
journal article
Language
en
Open access
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • Journal of Molecular Biology (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Science Foundation
  • National Institutes of Health
  • National Eye Institute (PN2EY016525)
  • National Institute of General Medical Sciences (R01GM079429, P41GM103832)
  • National Center for Research Resources (P41-RR-02250, P41RR002250)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
protein structure refinement, Rosetta, model rebuilding, homology modeling, atomic resolution
MeSH terms
Image Processing, Computer-Assisted, Proteins, Cryoelectron Microscopy

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