PDC: a highly compact file format to store protein 3D coordinates

Database (Oxford). 2023 Apr 3;2023:baad018. doi: 10.1093/database/baad018.

ABSTRACT

Recent improvements in computational and experimental techniques for obtaining protein structures have resulted in an explosion of 3D coordinate data. To cope with the ever-increasing sizes of structure databases, this work proposes the Protein Data Compression (PDC) format, which compresses coordinates and temperature factors of full-atomic and Cα-only protein structures. Without loss of precision, PDC results in 69% to 78% smaller file sizes than Protein Data Bank (PDB) and macromolecular Crystallographic Information File (mmCIF) files with standard GZIP compression. It uses ∼60% less space than existing compression algorithms specific to macromolecular structures. PDC optionally performs lossy compression with minimal sacrifice of precision, which allows reduction of file sizes by another 79%. Conversion between PDC, mmCIF and PDB formats is typically achieved within 0.02 s. The compactness and fast reading/writing speed of PDC make it valuable for storage and analysis of large quantity of tertiary structural data. Database URL https://github.com/kad-ecoli/pdc.

PMID:37010520 | PMC:PMC10069377 | DOI:10.1093/database/baad018