Journal of Biomolecular NMR

, Volume 57, Issue 1, pp 27–35 | Cite as

Improving 3D structure prediction from chemical shift data

  • Gijs van der Schot
  • Zaiyong Zhang
  • Robert Vernon
  • Yang Shen
  • Wim F. Vranken
  • David Baker
  • Alexandre M. J. J. Bonvin
  • Oliver F. Lange
Article

Abstract

We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50–100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 Å RMSD from the reference).

Keywords

Nuclear magnetic resonance Protein structure calculation CS-ROSETTA Sparse data 

Supplementary material

10858_2013_9762_MOESM1_ESM.pdf (5.2 mb)
Supplementary material 1 (PDF 5324 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Gijs van der Schot
    • 1
  • Zaiyong Zhang
    • 2
  • Robert Vernon
    • 3
  • Yang Shen
    • 4
  • Wim F. Vranken
    • 5
    • 6
  • David Baker
    • 3
    • 7
  • Alexandre M. J. J. Bonvin
    • 1
  • Oliver F. Lange
    • 2
    • 8
  1. 1.Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science—ChemistryUtrecht UniversityUtrechtThe Netherlands
  2. 2.Biomolecular NMR and Munich Center for Integrated Protein Science, Department ChemieTechnische Universität MünchenGarchingGermany
  3. 3.Department of BiochemistryUniversity of WashingtonSeattleUSA
  4. 4.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaUSA
  5. 5.Department of Structural BiologyVIBBrusselsBelgium
  6. 6.Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
  7. 7.Howard Hughes Medical InstituteUniversity of WashingtonSeattleUSA
  8. 8.Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany

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