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

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 3 compared to the next best method. Its reconstruction error of 0.08 Å is comparable to the best lossy compressor. It is 5 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 analyzing large collections of protein structures. Availability 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. Supplementary information Supplementary data is available at Bioinformatics online.

AlphaFold2 can predict single-mutation effects

“…All AF structures analyzed here are available at [48]. PDB files were compressed using Foldcomp [49]. "…”

Dual‐wield NTPases: A novel protein family mined from AlphaFold DB

“…By computationally scanning more than 214 million entries in AlphaFold DB version 4 (Kim et al, 2023 ; Varadi et al, 2024 ), we extracted 15,977 single‐chained structures possessing multiple P‐loops. We then analyzed the hydrogen‐bond network and extracted 839 structures with multiple P‐loops on a single continuous β‐sheet (Frishman & Argos, 1995 ).…”

Image-centric compression of protein structures improves space savings

“…Ultimately, we hope that this study points the way for future image-centric (or more generally structure-aware) compression of protein structures. Indeed, the contemporaneous Foldcomp [22] makes use of internal bond angles and torsions in protein compression, which is a different means of exploiting the 3D structure than our image-centric approach, and that shows greater promise even than PIC.…”

“…The coordinates are measured in units of Angstroms Å, where 1µm = 10, 000 Å [19]. Unlike their FASTA counterparts, comparatively less work has been done to create compressors customized for the structural data contained in PDB and mmCIF files, though there have been a number of recent tools/formats like MMTF [20], BCIF [21], and the brand new Foldcomp [22]. We note with especial interest Foldcomp, which introduces a new paradigm for compressing atomic coordinates using local angles, which is a radical shift from what both MMTF and BCIF do.…”