Paper Info
Title
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
Abstract
3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression-factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.
Year
DOI
Venue
2020
10.1371/journal.pcbi.1008247
PLOS COMPUTATIONAL BIOLOGY
DocType
Volume
Issue
Journal
16
10
ISSN
Citations 
PageRank 
1553-734X
0
0.34
References 
Authors
0
7
Name
Order
Citations
PageRank
David Sehnal1758.73
Sebastian Bittrich200.34
Torsten Schwede350042.56
Jaroslav Koca419325.16
Radka Svobodová Vareková57912.54
Stephen K. Burley623017.85
Rose Alexander S7565.54