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. BonvinEmail author
  • Oliver F. LangeEmail author


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).


Nuclear magnetic resonance Protein structure calculation CS-ROSETTA Sparse data 



This work was supported by the German Science Foundation (DFG) Grant LA 1817/3-1 (to Z.Z. and O.F.L.), the Brussels Institute for Research and Innovation (Innoviris) grant BB2B 2010-1-12 (to W.F.V.), and the Intramural Research Program of the NIDDK (to Y.S.). The WeNMR project (European FP7 e-Infrastructure Grant, Contract No. 261572,, supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands (via the Dutch BiG Grid project), Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the Latin America GRID infrastructure via the Gisela project is acknowledged for the use of web portals, computing and storage facilities.

Supplementary material

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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
    Email author
  • Oliver F. Lange
    • 2
    • 8
    Email author
  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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