IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-20177-1.html
   My bibliography  Save this article

A method for validating the accuracy of NMR protein structures

Author

Listed:
  • Nicholas J. Fowler

    (University of Sheffield)

  • Adnan Sljoka

    (RIKEN Center for Advanced Intelligence Project, RIKEN
    University of Toronto, UTM)

  • Mike P. Williamson

    (University of Sheffield)

Abstract

We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.

Suggested Citation

  • Nicholas J. Fowler & Adnan Sljoka & Mike P. Williamson, 2020. "A method for validating the accuracy of NMR protein structures," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20177-1
    DOI: 10.1038/s41467-020-20177-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-20177-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-20177-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Piotr Klukowski & Roland Riek & Peter Güntert, 2022. "Rapid protein assignments and structures from raw NMR spectra with the deep learning technique ARTINA," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Haohuai He & Bing He & Lei Guan & Yu Zhao & Feng Jiang & Guanxing Chen & Qingge Zhu & Calvin Yu-Chian Chen & Ting Li & Jianhua Yao, 2024. "De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-20177-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.