ArticleDatabase : the journal of biological databases and curation2023
PDC: a highly compact file format to store protein 3D coordinates.
Article in Database : the journal of biological databases and curation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
2 citing papers in PubMed, 2 citations in OpenAlex.
- FURNA: A database for functional annotations of RNA structures.PLoS biology · 2024Article
- Efficient protein structure archiving using ProteStAr.Bioinformatics (Oxford, England) · 2024Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
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