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Measuring similarity between dynamic ensembles of biomolecules

Nature Methods volume 11, pages 552–554 (2014)Cite this article

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Abstract

We present a simple and general approach termed REsemble for quantifying population overlap and structural similarity between ensembles. This approach captures improvements in the quality of ensembles determined using increasing input experimental data—improvements that go undetected when conventional methods for comparing ensembles are used—and reveals unexpected similarities between RNA ensembles determined using NMR and molecular dynamics simulations.

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Figure 1: Measuring population overlap and structural similarity between ensembles.
Figure 2: Comparing MD-generated and NMR RDC–selected ensembles of HIV-1 TAR.

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Acknowledgements

We thank members of the Al-Hashimi laboratory for critical comments on the manuscript. This work was supported by the US National Institutes of Health (R01AI066975 and PO1 GM0066275).

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Authors and Affiliations

  1. Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA

    Shan Yang

  2. Biophysics, University of Michigan, Ann Arbor, Michigan, USA

    Loïc Salmon

  3. Department of Biochemistry and Chemistry, Duke University School of Medicine, Durham, North Carolina, USA

    Hashim M Al-Hashimi

Authors
  1. Shan Yang
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  2. Loïc Salmon
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  3. Hashim M Al-Hashimi
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Contributions

S.Y., L.S. and H.M.A.-H. conceived the idea; S.Y. and L.S. carried out the data analysis with help from H.M.A.-H.; S.Y., L.S. and H.M.A.-H. wrote the paper.

Corresponding author

Correspondence to Hashim M Al-Hashimi.

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Competing interests

H.M.A.-H. is an advisor to and holds an ownership interest in Nymirum, an RNA-based drug discovery company.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 1631 kb)

Supplementary Software

Source code of SAS and ensemble similarity measurement (ZIP 95 kb)

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Yang, S., Salmon, L. & Al-Hashimi, H. Measuring similarity between dynamic ensembles of biomolecules. Nat Methods 11, 552–554 (2014). https://doi.org/10.1038/nmeth.2921

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