Skip to main content
SpringerLink
Log in

DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps

  • Correspondence
  • Published:

From Nature Methods

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: Overview of data stored in DAQ-Score Database.

Data availability

All precomputed DAQ score data are available at https://daqdb.kiharalab.org/. The DAQ-Score Database will be updated and maintained by the Kihara lab, with possible future assistance from system managers and other structural biology researchers at Purdue University.

Code availability

Source code for computing DAQ scores is available at https://github.com/kiharalab/DAQ.

References

  1. Berman, H. M. et al. Nucleic Acids Res. 28, 235–242 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Lawson, C. L. et al. Nucleic Acids Res. 44, D396–D403 (2016).

    Article  CAS  PubMed  Google Scholar 

  3. Lawson, C. L. et al. Nat. Methods 18, 156–164 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Terashi, G., Wang, X., Maddhuri Venkata Subramaniya, S. R., Tesmer, J. J. G. & Kihara, D. Nat. Methods 19, 1116–1125 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. DAQ-score Google Colab. https://bit.ly/daq-score (accessed 1 May 2023).

  6. DAQ Score software. GitHub https://github.com/kiharalab/DAQ (accessed 1 May 2023).

  7. Sehnal, D. et al. Nucleic Acids Res. 49, W431–W437 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are grateful to C. Christoffer for proofreading the manuscript. This database is currently financially supported by grants from the US National Institutes of Health (R01GM133840, 3R01GM133840-02S1). D.K. also acknowledges supports from the US National Science Foundation (CMMI1825941, MCB1925643, DBI2146026, IIS2211598, DMS2151678 and DBI2003635). X.W. is a recipient of a MolSSI graduate fellowship.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Purdue University, West Lafayette, IN, USA

    Tsukasa Nakamura, Genki Terashi & Daisuke Kihara

  2. Department of Computer Science, Purdue University, West Lafayette, IN, USA

    Xiao Wang & Daisuke Kihara

Authors
  1. Tsukasa Nakamura
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Genki Terashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Daisuke Kihara
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

D.K. conceived the study. T.N. designed and implemented the DAQ-Score Database. T.N. constructed datasets and T.N. and X.W. performed the computations. T.N., X.W., G.T. and D.K. analyzed the data. T.N. drafted the manuscript and D.K. edited it. All authors read and approved the manuscript.

Corresponding author

Correspondence to Daisuke Kihara.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work

Supplementary information

Supplementary Information

Supplementary Notes 1 and 2 and Supplementary Figs. 1–3

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nakamura, T., Wang, X., Terashi, G. et al. DAQ-Score Database: assessment of map–model compatibility for protein structure models from cryo-EM maps. Nat Methods 20, 775–776 (2023). https://doi.org/10.1038/s41592-023-01876-1

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-023-01876-1

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation