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

Graphical abstract

References

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

[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

[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

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

[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

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

[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

[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

[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

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

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.

Competing interests

The authors declare that they have no competing interests or financial conflicts to disclose.

Electronic supplementary material

Supplementary material is available in the online version of this article at journal.hep.com.cn and link.springer.com.

RIGHTS & PERMISSIONS

2025 Higher Education Press