DOI: 10.1093/bioinformatics/btg299. PDB file parser and structure class implemented in Python

PDB file parser and structure class implemented in Python

10.1093/bioinformatics/btg299

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. Availability: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Bibliography

Hamelryck, T., & Manderick, B. (2003). PDB file parser and structure class implemented in Python. Bioinformatics, 19(17), 2308â2310.

Authors 2

Thomas Hamelryck (first)
Bernard Manderick (additional)

References 0 Referenced 233

None

Dates

Type	When
Created	21 years, 9 months ago (Nov. 20, 2003, 12:37 p.m.)
Deposited	2 years, 7 months ago (Jan. 25, 2023, 1:16 p.m.)
Indexed	6 days, 8 hours ago (Aug. 26, 2025, 3 a.m.)
Issued	21 years, 9 months ago (Nov. 22, 2003)
Published	21 years, 9 months ago (Nov. 22, 2003)
Published Online	21 years, 9 months ago (Nov. 22, 2003)
Published Print	21 years, 9 months ago (Nov. 22, 2003)

Funders 0

None

BibTeX

@article{Hamelryck_2003, title={PDB file parser and structure class implemented in Python}, volume={19}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btg299}, DOI={10.1093/bioinformatics/btg299}, number={17}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Hamelryck, Thomas and Manderick, Bernard}, year={2003}, month=nov, pages={2308–2310} }

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