Foldcomp: a library and format for compressing and indexing large protein structure sets

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 4
• Main Authors: Kim, Hyunbin, Mirdita, Milot, Steinegger, Martin
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 03.04.2023
• Subjects: Algorithms; Applications Note; Data Compression - methods; Gene Library; Proteins; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad153

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.