ArticleBioinformatics (Oxford, England)2023
Foldcomp: a library and format for compressing and indexing large protein structure sets.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Systematic discovery of circular permutations across the protein universe using CIRPIN.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.Journal of chemical information and modeling · 2026Article
- Structural motif search across the protein universe with Folddisco.Nature biotechnology · 2026Article
- CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs.bioRxiv : the preprint server for biology · 2025Article
- Large protein databases reveal structural complementarity and functional locality.Nature communications · 2025Article
- BFVD-a large repository of predicted viral protein structures.Nucleic acids research · 2025Article
- Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.bioRxiv : the preprint server for biology · 2024Article
- Efficient protein structure archiving using ProteStAr.Bioinformatics (Oxford, England) · 2024Article
- Article
- Dual-wield NTPases: A novel protein family mined from AlphaFold DB.Protein science : a publication of the Protein Society · 2024Article
- Deep learning for protein structure prediction and design-progress and applications.Molecular systems biology · 2024Review
- Fast and accurate protein structure search with Foldseek.Nature biotechnology · 2024Article
- Image-centric compression of protein structures improves space savings.BMC bioinformatics · 2023Article
- How AlphaFold2 shaped the structural coverage of the human transmembrane proteome.Scientific reports · 2023Article
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Authors and funding
3 authors.
Funding
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Abstract
summaryHighly accurate protein structure predictors have generated hundreds of millions of protein structures; these pose a challenge in terms of storage and processing. Here, we present Foldcomp, a novel lossy structure compression algorithm, and indexing system to address this challenge. By using a combination of internal and Cartesian coordinates and a bi-directional NeRF-based strategy, Foldcomp improves the compression ratio by a factor of three compared to the next best method. Its reconstruction error of 0.08 Å is comparable to the best lossy compressor. It is five times faster than the next fastest compressor and competes with the fastest decompressors. With its multi-threading implementation and a Python interface that allows for easy database downloads and efficient querying of protein structures by accession, Foldcomp is a powerful tool for managing and analysing large collections of protein structures. AVAILABILITY AND IMPLEMENTATION: Foldcomp is a free open-source software (GPLv3) and available for Linux, macOS, and Windows at https://foldcomp.foldseek.com. Foldcomp provides the AlphaFold Swiss-Prot (2.9GB), TrEMBL (1.1TB), and ESMatlas HQ (114GB) database ready-for-download.
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