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PDB-assistant: an integrated Web tool for analyzing and editing PDBs

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References

  1. Hamelryck T, Manderick B. PDB file parser and structure class implemented in Python. Bioinformatics, 2003, 19(17): 2308–2310

    Article  Google Scholar 

  2. Zhang S, Krieger J M, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python. Bioinformatics, 2021, 37(20): 3657–3659

    Article  Google Scholar 

  3. Rodrigues J P G L M, Teixeira J M C, Trellet M, Bonvin A M J J. PDB-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved]. F1000Research, 2018, 7: 1961

    Article  Google Scholar 

  4. Buchan D W A, Jones D T. The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Research, 2019, 47(W1): W402–W407

    Article  Google Scholar 

  5. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel R D, Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 2003, 31(13): 3784–3788

    Article  Google Scholar 

  6. Gracy J, Chiche L. PAT: a protein analysis toolkit for integrated biocomputing on the Web. Nucleic Acids Research, 2005, 33(S2): W65–W71

    Article  Google Scholar 

  7. Alva V, Nam S Z, Söding J, Lupas A N. The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Research, 2016, 44(W1): W410–W415

    Article  Google Scholar 

  8. Cao Y, Song L, Miao Z, Hu Y, Tian L, Jiang T. Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation. Bioinformatics, 2011, 27(6): 785–790

    Article  Google Scholar 

  9. Zhang C, Shine M, Pyle A M, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods, 2022, 19(9): 1109–1115

    Article  Google Scholar 

  10. Rose A S, Hildebrand P W. NGL Viewer: a Web application for molecular visualization. Nucleic Acids Research, 2015, 43(W1): W576–W579

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant No. 81973243) and the National Human Genetic Resources Center, National Research Institute for Family Planning.

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Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China

    Yukun Zhao, Changsen Zhou, Jianhong Gan, Zhi-Xiong Xiao & Yang Cao

  2. National Human Genetic Resources Center, Beijing, 100081, China

    Jianbo Lu & Xu Ma

Authors
  1. Yukun Zhao
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  2. Changsen Zhou
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  3. Jianhong Gan
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  4. Zhi-Xiong Xiao
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  5. Jianbo Lu
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  6. Xu Ma
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  7. Yang Cao
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Corresponding authors

Correspondence to Jianbo Lu, Xu Ma or Yang Cao.

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Zhao, Y., Zhou, C., Gan, J. et al. PDB-assistant: an integrated Web tool for analyzing and editing PDBs. Front. Comput. Sci. 19, 193910 (2025). https://doi.org/10.1007/s11704-024-40577-6

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  • DOI: https://doi.org/10.1007/s11704-024-40577-6