PDBeCIF: an open-source mmCIF/CIF parsing and processing package

BMC Bioinformatics

José M. Dana¹  Sameer Velankar¹  Glen van Ginkel¹  Lukáš Pravda¹  Mihaly Varadi¹  Stephen Anyango¹  Peter Keller² 

[1] European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK;Global Phasing Ltd., Sheraton House, Castle Park, CB3 0AX, Cambridge, UK;

关键词: Software;    Parser;    PDB;    PDBx/mmCIF;    Protein structure;    CCD;    Small molecule;   

DOI  :  10.1186/s12859-021-04271-9

来源: Springer

【 摘 要 】

BackgroundBiomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread. Perhaps one of the reasons is the availability of easy to use tools that only support the legacy format, but also the inherent difficulties of processing mmCIF files correctly, given the number of edge cases that make efficient parsing problematic. Nevertheless, to fully exploit macromolecular structure data and their associated annotations such as multiscale structures from integrative/hybrid methods or large macromolecular complexes determined using traditional methods, it is necessary to fully adopt the new format as soon as possible.ResultsTo this end, we developed PDBeCIF, an open-source Python project for manipulating mmCIF and CIF files. It is part of the official list of mmCIF parsers recorded by the wwPDB and is heavily employed in the processes of the Protein Data Bank in Europe. The package is freely available both from the PyPI repository (http://pypi.org/project/pdbecif) and from GitHub (https://github.com/pdbeurope/pdbecif) along with rich documentation and many ready-to-use examples.ConclusionsPDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses.

【 授权许可】

CC BY