ArticlePLoS computational biology2020
BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Quantized neural representation for lossy cryo-EM compression.Bioinformatics (Oxford, England) · 2026Article
- RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.Nucleic acids research · 2026Article
- PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.Journal of molecular biology · 2025Article
- rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs.Journal of molecular biology · 2025Article
- MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.Nucleic acids research · 2025Article
- A Dataset for Investigations of Amine-Impregnated Solid Adsorbent for Direct Air Capture.Scientific data · 2025Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Mesoscale explorer: Visual exploration of large-scale molecular models.Protein science : a publication of the Protein Society · 2024Article
- Free tools for crystallographic symmetry handling and visualization.Journal of applied crystallography · 2024Article
- Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models.bioRxiv : the preprint server for biology · 2024Article
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.Journal of molecular biology · 2024Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- Efficient protein structure archiving using ProteStAr.Bioinformatics (Oxford, England) · 2024Article
- Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit.Current protocols · 2024Article
- RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.Bioinformatics (Oxford, England) · 2024Article
- Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.Current medicinal chemistry · 2024Review
- Image-centric compression of protein structures improves space savings.BMC bioinformatics · 2023Article
- RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.Journal of molecular biology · 2023Article
- ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.Journal of molecular biology · 2023Article
- Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.