foldcomp

name	foldcomp
description	Foldcomp — compress and index large protein structure sets (Steinegger lab) for efficient storage and random access before Foldseek-scale searches. Use when: (1) Archiving AFDB-scale PDB collections, (2) Reducing disk for structure search pipelines, (3) Extracting sequences/pLDDT from Foldcomp DBs. Upstream: https://github.com/steineggerlab/foldcomp. Route via homology-search with foldseek.
license	MIT
category	analysis-tools
tags	["Foldcomp","structure","compression","AFDB","Foldseek"]
upstream	https://github.com/steineggerlab/foldcomp
stage	function

Foldcomp

Upstream: steineggerlab/foldcomp

Citation

Kim, H., Mirdita, M. & Steinegger, M. Foldcomp: a library and format for compressing and indexing large protein structure sets. Bioinformatics 39, btad153 (2023). https://doi.org/10.1093/bioinformatics/btad153

See also docs/references.md.

Analytical thinking

Structure search needs structures on disk. Foldcomp provides a compact format + index for large PDB/mmCIF collections used with Foldseek-family tools. Infrastructure skill — not a homology algorithm itself.

How to run

# binaries: https://mmseqs.com/foldcomp  or pip package — see upstream
foldcomp compress input_structures/ structures.fcz
foldcomp decompress structures.fcz out_dir/
# subset decompress / extract AA or pLDDT — see upstream Usage

Decision tree

Many protein structures to store/search?
├─ Compress/index archive → foldcomp
├─ Search → foldseek / folddisco / foldmason
└─ Sequence-only path → foldseek + ProstT5

Related skills

foldseek · foldmason · folddisco · homology-search · tool-selection