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- Title
Foldcomp: a library and format for compressing and indexing large protein structure sets.
- Authors
Kim, Hyunbin; Mirdita, Milot; Steinegger, Martin
- Abstract
Summary: Highly 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.
- Subjects
PROTEIN structure; CARTESIAN coordinates; DATABASES; FREEWARE (Computer software); LINUX operating systems; IMAGE compression
- Publication
Bioinformatics, 2023, Vol 39, Issue 4, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btad153