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

Glen van Ginkel1, Lukáš Pravda1, José M Dana1

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BMC Bioinformatics
|July 24, 2021
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank (PDB) format is outdated; PDBeCIF is a new Python tool to process the PDBx/Macromolecular Crystallographic Information File (PDBx/mmCIF) format, enabling better use of structural data.

Keywords:
CCDPDBPDBx/mmCIFParserProtein structureSmall moleculeSoftware

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • The legacy Protein Data Bank (PDB) format is insufficient for current biomacromolecular structural data.
  • The PDBx/Macromolecular Crystallographic Information File (PDBx/mmCIF) format is the successor but its adoption is limited.
  • Difficulties in processing PDBx/mmCIF files and lack of supporting tools hinder widespread use.

Purpose of the Study:

  • To develop an efficient and accessible tool for manipulating PDBx/mmCIF files.
  • To facilitate the adoption of the PDBx/mmCIF format in the scientific community.
  • To support the analysis of complex structural data, including integrative/hybrid methods.

Main Methods:

  • Development of PDBeCIF, an open-source Python project.
  • Implementation of mmCIF and CIF file parsing capabilities.
  • Ensuring compatibility with Python 2.6+ and 3+.

Main Results:

  • PDBeCIF is an official mmCIF parser listed by the Worldwide Protein Data Bank (wwPDB).
  • The package is actively used in the Protein Data Bank in Europe (PDBe).
  • PDBeCIF is available on PyPI and GitHub with comprehensive documentation and examples.

Conclusions:

  • PDBeCIF is an efficient, lightweight, and dependency-free Python package.
  • It seamlessly integrates with third-party libraries.
  • PDBeCIF is suitable for broad scientific analyses and promotes the use of the PDBx/mmCIF format.