ArticlePloS one2017
Towards an efficient compression of 3D coordinates of macromolecular structures.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Fast and accurate protein structure search with Foldseek.Nature biotechnology · 2024Article
- Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data.BMC bioinformatics · 2024Article
- Image-centric compression of protein structures improves space savings.BMC bioinformatics · 2023Article
- Foldcomp: a library and format for compressing and indexing large protein structure sets.Bioinformatics (Oxford, England) · 2023Article
- PDC: a highly compact file format to store protein 3D coordinates.Database : the journal of biological databases and curation · 2023Article
- Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.Nucleic acids research · 2021Article
- Real-time structural motif searching in proteins using an inverted index strategy.PLoS computational biology · 2020Article
- BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management.PLoS computational biology · 2020Article
- BioJava 5: A community driven open-source bioinformatics library.PLoS computational biology · 2019Article
- NGL viewer: web-based molecular graphics for large complexes.Bioinformatics (Oxford, England) · 2018Article
- New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).Protein science : a publication of the Protein Society · 2018Article
- LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.Nature methods · 2017Article
- MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.PLoS computational biology · 2017Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.
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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.