Computing DAQ Score for a New Protein Model

DAQ score can be computed for a protein structure model built from a cryo-EM map on the Google Colab site or by downloading the software from the Github repository and run it locally.

Update History

    1. 2024/10/31: Entries were updated. (223,169 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/06/26.)
    2. 2024/09/24: Entries were updated. (217,989 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/05/29.)
    1. 2024/08/20: Entries were updated. (212,415 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/04/24.)
    2. Major update in the search engine. Now last names of "Deposition Author(s)" of entries are included as objects of a search.
    4. 2024/06/30: Entries were updated. (209,547 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/03/27.)
    5. 2024/05/31: Entries were updated. (205,353 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/02/28.)
    6. 2024/04/30: Entries were updated. (200,620 unique versioned chains. Based on the data in the Protein Data Bank as of 2024/01/31.)
    1. 2024/03/28: Entries were updated. (197,676 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/12/27.)
    2. URLs of minor updates of PDB entries are unified. For example, two minor versions of 7jsn_B, 22458_7jsn_B_v1 and 22458_7jsn_B_v1-0, are now redirected to 22458_7jsn_A_v1-1.
    3. Minor update in the search engine. Now a search for related entries, such as those for different chains/versions of an existing entry, are better performed from the existing entry ID as the query.
    8. 2024/02/29: Entries were updated. (194,757 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/11/29.)
    1. 2024/01/26: Added Download page.
    2. 2024/01/25: Changed notation of DAQ[ATOM] to DAQ[Cα].
    3. 2024/01/23: Entries were updated. (187,415 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/10/25.)
    10. 2023/12/14: Entries were updated. (184,772 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/09/27.)
    11. 2023/10/20: Entries were updated. (182,286 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/08/30.)
    12. 2023/10/19: Entries were updated. (177,876 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/07/26.)
    1. 2023/09/11: Entries were updated. (172,916 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/06/28.)
    2. 2023/09/11: For about 7% of entries, DAQ scores were somewhat revised. revised Entry ID list
    14. 2023/07/03: Entries were updated. (167,288 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/05/31.)
    15. 2023/05/31: Entries were updated. (162,355 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/04/26.)
    16. 2023/04/27: Entries were updated. (158,838 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/03/29.)
    17. 2023/03/13: Entries were updated. (152,129 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/02/08.)
    1. 2023/02/08: DAQ[Total] scores of some amount of entries were corrected.
    2. 2023/02/07: Entries were updated. (147,678 unique versioned chains. Based on the data in the Protein Data Bank as of 2023/01/11.)
    19. 2022/11/16: Entries were updated. (132,946 unique versioned chains. Based on the data in the Protein Data Bank as of 2022/08/24. Introduced the stricter threshold of the sum of cross correlation coefficient and overlap caused decreasing the number of chains.)
    20. 2022/09/28: Entries were updated. (143,221 unique versioned chains)
    21. 2022/06/22: The initial data was deposited. (8,710 unique chains)

References

To cite DAQ-Score Database, please use the following publication.

  1. Tsukasa Nakamura, Xiao Wang, Genki Terashi, and Daisuke Kihara, DAQ-Score Database: assessment of map-model compatibility for protein structure models from cryo-EM maps, Nature Methods 20, 775–776 (2023). LINK
    @article{nakamura2023daq, title={DAQ-Score Database: assessment of map--model compatibility for protein structure models from cryo-EM maps}, author={Nakamura, Tsukasa and Wang, Xiao and Terashi, Genki and Kihara, Daisuke}, journal={Nature Methods}, volume={20}, number={6}, pages={775--776}, year={2023}, }

To cite DAQ-score program, please use the following publication.

  1. Genki Terashi†, Xiao Wang†, Sai Raghavendra Maddhuri Venkata Subramaniya, John J. G. Tesmer, and Daisuke Kihara, Residue-Wise Local Quality Estimation for Protein Models from Cryo-EM Maps, Nature Methods 19, 1116-1125 (2022). LINK
    @article{genki2022DAQ, title={Residue-Wise Local Quality Estimation for Protein Models from Cryo-EM Maps}, author={Genki Terashi, Xiao Wang, Sai Raghavendra Maddhuri Venkata Subramaniya, John J. G. Tesmer, and Daisuke Kihara}, journal={Nature Methods}, year={2022} }

†Equal contribution

Contact

Daisuke Kihara (email: dkihara at purdue dot edu)

Kihara Lab.

DAQ-Score Database Team

Licenses

All of the data provided is available for academic use under a CC-BY-NC-4.0 license. by-nc

(For commercial use, please contact us for different licensing.)

All other contents on the DAQ-Score Database website are copyrighted.